Retrovirus detection

ABSTRACT

Provided are methods and compositions useful for detecting viral infection or contamination in a biological sample.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority under 35 U.S.C. 119 to U.S. Provisional Application Ser. Nos. 61/365,297, filed Jul. 16, 2010; 61/386,941, filed Sep. 27, 2010; and 61/391,360, filed Oct. 8, 2010, the disclosures of which are incorporated herein by reference.

TECHNICAL FIELD

The invention relates to methods and compositions useful for the detection of retroviruses in a subject or sample.

BACKGROUND

Xenotropic murine leukemia virus-related virus (XMRV) is a recently discovered human gammaretrovirus that resembles a xenotropic MLV, but that is distinguishable from xenotropic MLV in the sequence in its envelope (Urisman et al., PLOS pathogens 2(3):e25, 2006; and Dong et al. PNAS 104:1655, 2007). All isolates so far examined are highly homologous to each other (>98% sequence identity) and allow the distinction from xenotropic MLV. The reason for this sequence conservation is not currently understood. The original infectious clone is called XMRV VP62 (GenBank accession no. EF185282).

XMRV was originally described in association with prostate cancer and further connections have been suggested (R. Schlaberg et al. PNAS 2009, doi_(—)10.1073_pnas.0906922106), with 6-23% of prostate cancer patients testing positive. In addition, V. C. Lombardi et al. (Science 2009 doi10.1126/science.1179052) showed a possible association with chronic fatigue syndrome, with 67% of patients testing positive, compared to 3.7% of normals. Overall estimates of the prevalence in the general population from investigators in the USA range from 2-4%. However several recent studies in Europe have failed to detect XMRV in similar frequencies or similar associations (Fischer et al. Journal of Clinical Virology 43: 277-283 2008; Hohn et al. Retrovirology 6:92 2009; F J M van Kuppeveld et al., BMJ 340:c1018, 2010). Fischer et al. found 1 of 105 prostate cancer patients and 1 of 70 control subjects to be XMRV positive in a German study. Hohn et al. screened 589 prostate cancer patients in Germany without detecting a single positive. Van Kuppeveld et al. also failed to detect any DNA or RNA positives in 32 chronic fatigue patients or in 42 matched controls in Holland. Recently another paper from Fischer et al. (Emerg Infect Dis. 2010) showed about 10% positivity in RNA derived from sputum of 162 immunosuppressed patients and 2-3% positivity in sputum RNA from 168 normal patients in a German study. The assays did not appear to be different and no explanation was offered for the discrepancies.

The inconsistency of results calls into question the reliability of the current testing methods, in particular in DNA amplification. Following the lead of Lombardi et al. all investigators so far have used nested PCR using XMRV sequence based primers, followed by running the sample on a gel and looking for a visible band. This method is known to be variable in sensitivity and depend on the quality of nucleic acid samples. Detection of XMRV RNA has also been described mainly using the method of Dong et al. PNAS 2007, based on that of Urisman et al. 2006. In this assay RNA is prepared from tissue and/or blood, reverse transcribed to cDNA and the cDNA examined by QPCR with XMRV specific primers. As noted this led to inconsistent results (Enserink et al., Science 329:18-19, 2010). Claims of various sensitivities have been made for such tests, but it is not possible to verify any of these and the assays appear to be incompletely characterized.

A PCR based diagnostic screening assay for XMRV in human blood has been recently developed (www[.]vipdx.com), using nested PCR and gel detection of the amplification product (Lombardi et al.), with an estimated sensitivity for the nested DNA PCR around 600 proviral copies/test. In addition the report of Lombardi et al. do not show complete concordance of gag and env detection, with positives in gag and negatives for env observed in some subjects. This was attributed to variability in the assay. In all of the assays developed so far great care has been taken to use primers that will differentiate MLV from XMRV, so that only XMRV is detected. Therefore there is a great need for a reliable and validated assay for XMRV DNA and RNA in accessible samples from volunteers or patients in order to determine the real frequencies of positivity and whether there is linkage to disease. In addition a reliable blood screening assay is not available. Recent data suggest that detection of XMRV in many cases is caused by artifacts (Paprotka T., Science, 333, 97-101, 2011) or contamination with mouse DNA (Robinson M J. et al., Retrovirology, 7:108 doi:10.1186/1742-4690-7-108, 2010).

Furthermore, gene therapy vectors based upon MLV are being used including replication competent MLV-based vectors. For example, a replicating retrovirus based on amphotropic MLV and carrying an extra cytosine deaminase gene as a therapeutic agent for cancer including primary brain cancer leading to glioblastoma multiforme (GBM) (Tai et al., Mol. Ther., 12:842-851 2005; http:(//)oba.od.nih.gov/oba/RAC/meetings/Jun2009/976_Aghi.pdf; WO2010036986) having been used. An exemplary vector is being developed by Tocagen Inc. (San Diego, Calif.) and is referred to as Toca 511 (clinical trials.gov trial# NCT01156584). Subsequent to Toca 511 administration, patients are dosed with 5-fluorocytosine that is converted in situ to 5-fluorouracil, a potent anticancer compound. As the virus is generally only able to replicate in the tumor, this results in a very specific anti-cancer effect. In order to determine whether there is replication outside the tumor, for safety and/or for correlation with efficacy assays for detection of proviral DNA in the blood and MLV RNA in the plasma are needed. FDA currently requires follow-up on patients undergoing such investigational therapies with an integrating viral vector for 15 years post-treatment (Guidance for Industry—Supplemental Guidance on Testing for Replication Competent Retrovirus in Retroviral Vector Based Gene Therapy Products and During Follow-up of Patients in Clinical Trials Using Retroviral Vectors: FDA Center for Biologics Evaluation and Research November 2006; http://www.fda.gov/BiologicsBloodVaccines/GuidanceComplianceRegulatoryInformation/Guidances/CellularandGeneTherapy/ucm072961.htm). Assays are needed to accomplish this and a generally accepted marker for risk of disease and disease progression in viral diseases in general and retroviral diseases in particular is the levels over time of virus in the blood or in blood cells (Gurunathan S, Habib R E, et al. Vaccine. 2009; 27:1997-2015; Low A., Okeoma C M. et al. Virology 2009; 385: 455-463). On the other hand, replication of the virus in the tumor may leak into the periphery and blood stream and so assays that monitor the appearance and levels of viral sequence in the blood as DNA or RNA can be used to determine whether there is an effective treatment and whether there is a need to modify the treatment protocol, for example to read minister the viral vector or to use adjuvants (such as steroids) that will facilitate the viral replication in the tumor.

SUMMARY

The disclosure provides oliogonucleotide primers and probes for amplification and detection of MLV-related polynucleotides in a sample, tissue or subject. In one embodiment, the disclosure provides primers that can amplify multiple strains of MLV and XMRV and probe that can detect either or both of MLV or XMRV. In another embodiment, the disclosure provides primers and probes for monitoring subject undergoing treatment with a replication competent retrovirus expressing a heterologous gene such as cytosine deaminase. In this embodiment, the “companion” diagnostic is used to insure efficacy, expression, spread and long term infection of a vector used in such treatment.

The disclosure thus provides an isolated oligonucleotide consisting of a sequence selected from the group consisting of: SEQ ID NO:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 or any sequence set forth in Table 1 or 2 and oligonucleotides that are at least 95% identical to any of the foregoing and can hybridize to an MLV-related polynucleotide. In some embodiment, the primers and probes may differ from the foregoing or listed sequences in table 1 and 2 by 1-10 nucleotides at either the 5′ and/or 3′ end. In another embodiment, a primer pair consisting of SEQ ID NO:1 and 2 and sequence that are at least 95% identical to SEQ ID NO:1 and 2 and hybridize to an MLV-related polynucleotide. In yet another embodiment, a primer pair consisting of SEQ ID NO:4 and 5 and sequence that are at least 95% identical to SEQ ID NO:4 and 5 and hybridize to an MLV-related polynucleotide. In yet another embodiment, a primer pair consisting of SEQ ID NO:7 and 8 and sequence that are at least 95% identical to SEQ ID NO:7 and 8 and hybridize to an MLV-related polynucleotide. In yet another embodiment, a primer pair consisting of SEQ ID NO:10 and 11 and sequence that are at least 95% identical to SEQ ID NO:10 and 11 and hybridize to an MLV-related polynucleotide. In yet another embodiment, a primer pair consisting of SEQ ID NO:13 and 14 and sequence that are at least 95% identical to SEQ ID NO:13 and 14 and hybridize to an MLV-related polynucleotide. In yet another embodiment, a primer pair consisting of SEQ ID NO:16 and 17 and sequence that are at least 95% identical to SEQ ID NO:16 and 17 and hybridize to an MLV-related polynucleotide. In yet another embodiment, a primer pair consisting of SEQ ID NO:19 and 20 and sequence that are at least 95% identical to SEQ ID NO:19 and 20 and hybridize to an MLV-related polynucleotide. In yet another embodiment, the oligonucleotide comprises a primer chose from regions of homology between XMRV and MLV.

The disclosure also provides a method of determining viral content in a subject about to undergo or undergoing a retroviral gene delivery therapy using an MLV-related virus, comprising:obtaining a sample from the subject; contacting the sample with one or more primer pairs as set forth above under conditions suitable for nucleic acid amplification to obtain amplified products; contacting the sample with a one or more probes that hydridizes to the amplified product; detecting a hybridized product; indicating that the subject has viral content comprising an MLV-related virus. In one embodiment, the MLV-related virus is a recombinant retroviral vector used in gene delivery. In another embodiment, the MLV-related virus is an XMRV virus. In yet another embodiment, the method is carried out prior to delivery of a MLV-related retroviral vector for gene delivery. In yet another embodiment, the method is carried out following delivery of a MLV-related retroviral vector for gene delivery. In another embodiment,

the MLV-related virus comprises a 5′ LTR, gag, pol, env genes, a regulatory domain 3′ of the env gene linked to a heterologous polynucleotide to be delivered and a 3′ LTR and a promoter for expression in mammalian cells in the 5′LTR. In another embodiment, the regulatory domain is an internal ribosome entry site (IRES). In yet another embodiment, the heterologous polynucleotide encodes a polypeptide having cytosine deaminase activity. In embodiments and described above, the method monitors the spread of the MLV-related retroviral vector. In another embodiment, the method is carried out routinely over the course years.

The disclosure also provides a method for detecting the presence of a viral agent in a sample comprising: measuring the amount of a polynucleotide in a sample using a quantitative polymerase chain reaction or other amplification process comprising oligonucleotide primer/probe combinations selected from the group consisting of: (i) SEQ ID NO: 1, 2 and 3; (ii) SEQ ID NO: 4, 5 and 6; (iii) SEQ ID NO: 7, 8 and 9; (iv) SEQ ID NO: 10, 11 and 12; and (v) primer pairs according to claim 9 and corresponding probes that have at least 95% identity to both XMRV and MLV. In one embodiment, the polynucleotide is DNA or RNA.

In various embodiments above, the quantitating and amplification are performed by quantitative polymerase chain reaction, e.g., RT-qPCR. In any of the foregoing methods the measuring detects a single copy of a viral agent related nucleic acid. In any of the foregoing embodiments, the sample can be a mammalian tissue (e.g., blood). In any of the foregoing embodiments a viral agent to be detected can be a gene therapy vector. In one embodiment, the gene therapy vector is a replication-competent vector. In another embodiment, the method is performed prior to a therapeutic regimen comprising a gene therapy vector treatment. In yet another embodiment, the method is performed subsequent to a therapeutic regimen comprising gene therapy vector on a subject. The method can be performed to monitor the dosage of a therapeutic regimen comprising a gene therapy vector in a subject. In yet another embodiment, the gene therapy vector comprises a replication competent MLV vector. In yet another embodiment, the method is performed prior to a therapeutic regimen comprising a gene therapy vector. In one embodiment, the method is performed subsequent to a therapeutic regimen comprising a gene therapy vector. In yet another embodiment, the method is performed to monitor the dosage of a therapeutic regimen comprising a gene therapy vector.

The disclosure also provides kits for carrying out any of the foregoing methods and comprising any of the oligonucleotides compositions of the disclosure (e.g., SEQ ID NO:1-21, Table 1 and 2).

The disclosure also provides a method for detecting <100 copies of MLV related DNA in a sample extracted from fixed histopathological sections. The disclosure also provides a method for detecting <100 copies of MLV related RNA in a sample extracted from fixed histopathological sections.

The disclosure also provides a method that detects both MLV and XMRV and variants thereof. In other embodiment, the method detects only MLV related virus and does not detect XMRV. In certain embodiment, the method detects XMRV gag and MLV gag. In yet other embodiment, the method detects XMRV pol and MLV pol. The disclosure provides methods that detects XMRV Env and MLV Env. The disclosure also provides methods for detecting either XMRV or MLV related virus in plasma or serum from a mammalian host.

The disclosure provides a method of selectively detecting MLV related viruses in humans and which does not detect XMRV comprising primers selected from the group consisting of: SEQ ID NO:10 and 11; SEQ ID NO:13 and 14; SEQ ID NO:16 and 17; SEQ ID NO:19 and 20; sequences at least 95% identical to the foregoing; and combination thereof, using the methods described herein.

The disclosure also provides a method of determining whether a human subject is at risk of having prostate cancer or chronic fatigue syndrome comprising utilizing primer pairs and probes as set forth in SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 or primer/probes as set forth in Table 1 or 2, to amplify polynucleotides in a sample from the subject, wherein the presence of an amplified product is indicative of a risk of prostate cancer or chronic fatigue syndrome.

The disclosure also provides a method of screening a blood supply or tissue bank for infection by an MLV, MLV-variant or XMRV comprising performing an amplification reaction on the blood supply or tissue bank utilizing primers as set forth in SEQ ID NO:4, 5, 7, 8, 10, 11, 13, 14, or any of the primers in Table 1 or 2, and detecting an amplified product.

The disclosure is directed to the detection of xenotropic murine leukemia virus related virus (XMRV) or other retroviruses related to murine leukemia viruses that can be present in human tissue blood or serum. In particular, the disclosure relates to sensitive reliable quantitative PCR assays for the detection of XMRV provirus in DNA from blood of human and animal subjects and for the sensitive and reliable detection of XMRV RNA (potentially from viral particles) from plasma or serum of human and animal subject by reverse transcription (RT) and polymerase chain reaction. In one embodiment, the quantitative assay is a TaqMan® assay using the primers and probes constructed based on the genome of the XMRV virus. In contrast to other techniques using XMRV specific primer/probe sets and avoiding primer/probe sets with homology to MLV, the disclosure constructed PCR based assays that detect MLV related viruses that may or may not be XMRV in human samples, by using MLV specific qPCR primers and probes, that also detect XMRV. Such assays are useful in combination with assays for MLV sequences that are not homologous to XMRV to determine if recombination has occurred in patients treated with replication competent retroviruses, who may also be positive for XMRV. The disclosure further relates to a diagnostic kit that comprises nucleic acid molecules for the detection of the XMRV and MLV related viruses. In addition, for detection of MLV vectors when monitoring of patients treated with MLV related vectors, diagnostic kits that detect the transgene carried by the MLV vector are also disclosed.

The details of one or more embodiments of the disclosure are set forth in the accompanying drawings and the description below. Other features, objects, and advantages will be apparent from the description and drawings, and from the claims.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 shows XMRV gag standard in pUC57-XMRV gag plasmid DNA. The insert corresponds to nucleotides 628 to 764 of the XMRV VP62 clone sequence (NC_(—)007815). The derived sequence is synthesized by BioBasic Inc and inserted into pUC57 backone at SmaI site between BamHI and ApaI sites.

FIG. 2 shows XMRV env standard sequence in pET28b-XMRV env plasmid DNA. The insert corresponds to nucleotides 6252 to 6391 of the XMRV VP62 clone sequence (NC_(—)007815). The derived sequence is synthesized by BioBasic Inc and inserted into pET28b+ backone at EcoRV site between BssHI and HpaI sites.

FIG. 3 shows the MLV pol1 and pol2 standard sequences in pAZ3-emd plasmid DNA which encodes an ecotropic Moloney MLV gag-pol, amphotropic env and IRES-GFPemd cassette downstream of the env (Logg et al. J. Virol. 75:6989-6998, 2001.

FIG. 4 shows a comparison of the sequences of Toca 511 (the proviral form) used to treat GBM patients and an XMRV provirus (VP 62, NCBI Reference Sequence NC_(—)007815.1), noting the overall homology of the LTR, gag, pol and envelope regions. Also shown are the regions of the pol1 and pol2 amplicons. The MLV pol1 and pol2 standard sequences in pAZ3-emd plasmid DNA.

FIG. 5 shows a BLAST nucleic acid sequence comparison of the sequence of XMRV (VP62, NCBI ref. NC_(—)007815.1, Sbjct) and MoMLV (NCBI ref. NC_(—)001501.1, Query), showing sequences of 20 or more nucleotides that are exactly homologous (underlined/highlighted).

FIG. 6 shows XMRV gag standard in pUC57-XMRV gag plasmid DNA amplification curves from 1E0 to 1E7.

FIG. 7 shows XMRV env standard in pET28b-XMRV env plasmid DNA amplification curves from 1E0 to 1E7.

FIG. 8A-C shows a) 1-Stage qPCR Protocol: pUC57-XMRV gag plasmid standard targeted with XMRV gag primer/probe set. pUC57-XMRV gag plasmid DNA in TE was targeted with XMRV gag primers and a 1-stage qPCR protocol was performed. The mean Ct and standard deviation was calculated; b) shows 1-Stage qPCR Protocol: Controls targeted with XMRV gag primer/probe set. 22Rv1 gDNA positive control, naïve human blood gDNA negative control and NTC were targeted with the XMRV gag primer/probe set and a 1-stage qPCR protocol was performed. The mean Ct, standard deviation and copies/reaction were calculated. ‘ND’ means ‘non-detected’; c) shows 1-Stage qPCR Protocol: Spiked human blood gDNA targeted with XMRV gag primer/probe set. Neat human blood gDNA was spiked with 8 log concentrations of pUC57-XMRV gag plasmid DNA (1E0 to 1E8 copies/reaction). The samples were targeted with the XMRV gag primer/probe set and a 1-stage qPCR protocol was performed. The mean Ct, standard deviation, copies/reaction and % recovery of the input copies/reaction were determined (the % recovery was determined by using the following equation: detected copies/reaction divided by the input copies/reaction times 100).

FIG. 9A-C shows a) 1-Stage qPCR Protocol: pET28b-XMRV env plasmid standard targeted with XMRV env primer/probe set. pET28b-XMRV env plasmid DNA in TE was targeted with XMRV env primers and a 1-stage qPCR protocol was performed. The mean Ct and standard deviation was calculated; b) shows 1-Stage qPCR Protocol: Controls targeted with XMRV env primer/probe set. 22Rv1 gDNA positive control, naïve human blood gDNA negative control and NTC were targeted with the XMRV env primer/probe set and a 1-stage qPCR protocol was performed. The mean Ct, standard deviation and copies/reaction were calculated. ‘ND’ means ‘non-detected’; c) shows 1-Stage qPCR Protocol: Spiked human blood gDNA targeted with XMRV env primer/probe set. Neat human blood gDNA was spiked with 8 log concentrations of pET28b-XMRV env plasmid DNA (1E0 to 1E8 copies/reaction). The samples were targeted with the XMRV env primer/probe set and a 1-stage qPCR protocol was performed. The mean Ct, standard deviation, copies/reaction and % recovery of the input copies/reaction were determined (the % recovery was determined by using the following equation: detected copies/reaction divided by the input copies/reaction times 100).

FIG. 10A-C shows a) 1-Stage qPCR Protocol: pAZ3-emd pol2 plasmid standard targeted with XMRV pol2 primer/probe set. pAZ3-emd pol2 plasmid DNA in TE was targeted with XMRV pol2 primers and a 1-stage qPCR protocol was performed. The mean Ct and standard deviation was calculated; b) shows 1-Stage qPCR Protocol: Controls targeted with XMRV pol2 primer/probe set. 22Rv1 gDNA positive control, and naïve human blood gDNA negative control were targeted with the XMRV pol2 primer/probe set and a 1-stage qPCR protocol was performed. The mean Ct, standard deviation and copies/reaction were calculated. ‘ND’ means ‘non-detected’; c) shows 1-Stage qPCR Protocol: Spiked human blood gDNA targeted with XMRV pol2 primer/probe set. Neat human blood gDNA was spiked with 8 log concentrations of pAZ3-emd pol2 plasmid DNA (1E0 to 1E8 copies/reaction). The samples were targeted with the XMRV pol2 primer/probe set and a 1-stage qPCR protocol was performed. The mean Ct, standard deviation, copies/reaction and % recovery of the input copies/reaction were determined (the % recovery was determined by using the following equation: detected copies/reaction divided by the input copies/reaction times 100).

FIG. 11A-B shows a) 0-Stage vs. 1-Stage qPCR Protocols: pUC57 XMRV gag Standards. A 0-stage and a 1-stage qPCR protocol were performed targeting the pUC57 XMRV gag plasmid using XMRV gag primers. ‘pUC57 XMRV gag’ means the number of pUC57 XMRV gag copies spiked into a single qPCR reaction; b) shows 0-Stage vs. 1-Stage qPCR Protocols: pUC57 XMRV gag spike-ins into CA Human Blood gDNA. A 0-Stage and a 1-stage qPCR protocol were performed targeting pUC57 XMRV gag spike-ins into CA human blood gDNA and using XMRV gag primers. ‘pUC57 XMRV gag/001 gDNA’ means the number of pUC57 XMRV gag copies spiked into donor 001 gDNA in a single qPCR reaction; ‘001’ means ‘donor #001’; ‘ND’ means ‘non-detected’.

FIG. 12A-B shows a) 0-Stage vs. 1-Stage qPCR Protocols: pET28b XMRV env Standards. A 0-stage and a 1-stage qPCR protocol were performed targeting the pET28b XMRV env plasmid using XMRV env primers. ‘pET28b XMRV env’ means the number of pET28b XMRV env copies spiked into a single qPCR reaction; b) shows 0-Stage vs. 1-Stage qPCR Protocols: pET28b XMRV env spike-ins into 001 Human Blood gDNA. A 0-stage and a 1-stage qPCR protocol were performed targeting pET28b XMRV env spike-ins into 001 human blood gDNA and using XMRV env primers. ‘pET28b XMRV env /001 gDNA’ means the number of pET28b XMRV env copies spiked into donor 001 gDNA in a single qPCR reaction; ‘001’ means ‘donor #001’; ‘ND’ means ‘non-detected’.

FIG. 13A-B shows a) 0-Stage vs. 1-Stage qPCR Protocols: pAZ3-emd pol2 standards. A 0-Stage and a 1-stage qPCR protocol were performed targeting the pAZ3-emd pol2 plasmid using XMRV pol2 primers. ‘pAZ3-emd pol2’ means the number pAZ3-emd pol2 copies spiked into a single qPCR reaction; ‘ND’ means ‘non-detected’; b) Shows 0-Stage vs. 1-Stage qPCR Protocols: pAZ3-emd pol2 spike-ins into 001 Human Blood gDNA. A 0-Stage and a 1-stage qPCR protocol were performed targeting pAZ3-emd pol2 spike-ins into 001 human blood gDNA and using XMRV pol2 primers. ‘pAZ3-emd pol2/001 gDNA’ means the number of pAZ3-emd pol2 copies spiked into donor 001 gDNA in a single qPCR reaction; ‘001’ means ‘donor #001’; ‘ND’ means ‘non-detected’

FIG. 14 shows detection of MLV using MLV and ENV2 primer sets from formalin fixed paraffin embedded tissue (FFPE) infected with MLV. Paz3-emd spike in was added to either 100 ng fresh tumor sample that was frozen or added to 100 ng of a FFPE DNA tumor sample. qPCR was performed with the MLV and ENV2 primer sets.

FIG. 15 shows detection of XMRV in whole blood by RTPCR using XMRV specific primer sets XMRV gag, XMRV pol2, XMRV env.

FIG. 16A-B shows the results of monitoring patients over time with assays described herein for provirus DNA (MLVLTR primers and probes) in whole blood DNA, for viral RNA (by env RT-PCR) in the plasma, and for antiviral antibody responses in the plasma. These subjects (recurrent Glioblastoma multiforme (GBM) patients) were treated by intracranial injection of 2.6×10³ TU/g brain of T5.0002 amphotropic MLV retrovirus encoding a modified yeast cytosine deaminase (WO2010036986, WO2010045002) followed by 5-fluorocytosine treatment courses at approximately 130 mg/kg/day. (A) patient 101; (B) patient 102.

DETAILED DESCRIPTION

Also, the use of “or” means “and/or” unless stated otherwise. Similarly, “comprise,” “comprises,” “comprising” “include,” “includes,” and “including” are interchangeable and not intended to be limiting.

It is to be further understood that where descriptions of various embodiments use the term “comprising,” those skilled in the art would understand that in some specific instances, an embodiment can be alternatively described using language “consisting essentially of” or “consisting of.”

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this disclosure belongs. Although any methods and reagents similar or equivalent to those described herein can be used in the practice of the disclosed methods and compositions, the exemplary methods and materials are now described.

As used herein and in the appended claims, the singular forms “a,” “and,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “an oligonucleotide” includes a plurality of such oligonucleotides and reference to “the polynucleotide” includes reference to one or more polynucleotides known to those skilled in the art, and so forth.

The detection of XMRV or MLV related retroviruses by nucleic acid amplification techniques in human or animal tissues, blood or plasma/serum is of use for determining prostate cancer and risk thereof, chronic fatigue system and risk thereof, contamination of blood supply and tissue donation material and in following the status of subjects undergoing therapy with an MLV derived therapeutic virus comprising a heterologous genetic sequence such as, for example, an engineered retroviral replicatog virus based on amphotropic MLV (e.g., Toca 511). For example, the methods and compositions of the disclosure can be used to monitor therapy with an retroviral vector comprising sequences with substantial identity to MLV, in determining if recombination takes place between the therapeutic vector and XMRV or other MLV related natural infections, and for determining if a subject carries XMRV or another MLV related naturally occurring virus. Such assays are also useful for screening the blood supply to exclude subjects that are positive for XMRV or other MLV related retroviruses. Such assays also can be used to determine levels of MLV related virus over time, and provide information when it would be useful to start administering antiretroviral therapies that are also active against MLV such as, for example, AZT (Sakuma et al., Virology, 2009; Powell et al., J. Virol., 73:8813-8816, 1999; G. B. Beck-Engeser, PNAS, 2009). Such assays when used with histopathology samples can be used to determine the presence or absence of XMRV or other MLV related retroviruses in a patients stored sample or to determine the epidemiology of the XMRV or MLV related virus. Such assays can also be used to monitor patients to whom therapeutic vectors based on replicating MLV vectors have been administered. These measurements can be used to track the safety of the therapy over time (e.g., to 15 years and beyond) as high persistent levels (greater than 30,000, 100,000 or 300,000 copies/microgram) of MLV in genomic DNA or greater than 30,000 100,000 or 300,000 RNA copies/ml plasma) or increasing levels of these over time, can be used as a signal to more closely monitor for diseases that could be secondary to a therapy using an gene therapy vector comprising MLV or MLV-related sequences, such as leukemia or to start antiretroviral therapy. However, these measurements can also be used to judge the extent of replication of the MLV or MLV-related vector in a target tissue (i.e., efficacy or susceptibility to successful treatment) because of the possibility of “spill” into the circulatory system. Other uses of these assays for clinical monitoring will be apparent to those skilled in the art.

Engineered retroviral vectors that can be monitored include those set forth below:

RCR Vector - pAC-yCD2 tagttattaa tagtaatcaa ttacggggtc attagttcat agcccatata tggagttccg cgttacataa cttacggtaa atggcccgcc tggctgaccg cccaacgacc cccgcccatt gacgtcaata atgacgtatg ttcccatagt aacgccaata gggactttcc attgacgtca atgggtggag tatttacggt aaactgccca cttggcagta catcaagtgt atcatatgcc aagtacgccc cctattgacg tcaatgacgg taaatggccc gcctggcatt atgcccagta catgacctta tgggactttc ctacttggca gtacatctac gtattagtca tcgctattac catggtgatg cggttttggc agtacatcaa tgggcgtgga tagcggtttg actcacgggg atttccaagt ctccacccca ttgacgtcaa tgggagtttg ttttggcacc aaaatcaacg ggactttcca aaatgtcgta acaactccgc cccattgacg caaatgggcg gtaggcgtgt acggtgggag gtctatataa gcagagctgg tttagtgaac cggcgccagt cctccgattg actgagtcgc ccgggtaccc gtgtatccaa taaaccctct tgcagttgca tccgacttgt ggtctcgctg ttccttggga gggtctcctc tgagtgattg actacccgtc agcgggggtc tttcatttgg gggctcgtcc gggatcggga gacccctgcc cagggaccac cgacccacca ccgggaggta agctggccag caacttatct gtgtctgtcc gattgtctag tgtctatgac tgattttatg cgcctgcgtc ggtactagtt agctaactag ctctgtatct ggcggacccg tggtggaact gacgagttcg gaacacccgg ccgcaaccct gggagacgtc ccagggactt cgggggccgt ttttgtggcc cgacctgagt ccaaaaatcc cgatcgtttt ggactctttg gtgcaccccc cttagaggag ggatatgtgg ttctggtagg agacgagaac ctaaaacagt tcccgcctcc gtctgaattt ttgctttcgg tttgggaccg aagccgcgcc gcgcgtcttg tctgctgcag catcgttctg tgttgtctct gtctgactgt gtttctgtat ttgtctgaga atatgggcca gactgttacc actcccttaa gtttgacctt aggtcactgg aaagatgtcg agcggatcgc tcacaaccag tcggtagatg tcaagaagag acgttgggtt accttctgct ctgcagaatg gccaaccttt aacgtcggat ggccgcgaga cggcaccttt aaccgagacc tcatcaccca ggttaagatc aaggtctttt cacctggccc gcatggacac ccagaccagg tcccctacat cgtgacctgg gaagccttgg cttttgaccc ccctccctgg gtcaagccct ttgtacaccc taagcctccg cctcctcttc ctccatccgc cccgtctctc ccccttgaac ctcctcgttc gaccccgcct cgatcctccc tttatccagc cctcactcct tctctaggcg ccaaacctaa acctcaagtt ctttctgaca gtggggggcc gctcatcgac ctacttacag aagacccccc gccttatagg gacccaagac cacccccttc cgacagggac ggaaatggtg gagaagcgac ccctgcggga gaggcaccgg acccctcccc aatggcatct cgcctacgtg ggagacggga gccccctgtg gccgactcca ctacctcgca ggcattcccc ctccgcgcag gaggaaacgg acagcttcaa tactggccgt tctcctcttc tgacctttac aactggaaaa ataataaccc ttctttttct gaagatccag gtaaactgac agctctgatc gagtctgttc tcatcaccca tcagcccacc tgggacgact gtcagcagct gttggggact ctgctgaccg gagaagaaaa acaacgggtg ctcttagagg ctagaaaggc ggtgcggggc gatgatgggc gccccactca actgcccaat gaagtcgatg ccgcttttcc cctcgagcgc ccagactggg attacaccac ccaggcaggt aggaaccacc tagtccacta tcgccagttg ctcctagcgg gtctccaaaa cgcgggcaga agccccacca atttggccaa ggtaaaagga ataacacaag ggcccaatga gtctccctcg gccttcctag agagacttaa ggaagcctat cgcaggtaca ctccttatga ccctgaggac ccagggcaag aaactaatgt gtctatgtct ttcatttggc agtctgcccc agacattggg agaaagttag agaggttaga agatttaaaa aacaagacgc ttggagattt ggttagagag gcagaaaaga tctttaataa acgagaaacc ccggaagaaa gagaggaacg tatcaggaga gaaacagagg aaaaagaaga acgccgtagg acagaggatg agcagaaaga gaaagaaaga gatcgtagga gacatagaga gatgagcaag ctattggcca ctgtcgttag tggacagaaa caggatagac agggaggaga acgaaggagg tcccaactcg atcgcgacca gtgtgcctac tgcaaagaaa aggggcactg ggctaaagat tgtcccaaga aaccacgagg acctcgggga ccaagacccc agacctccct cctgacccta gatgactagg gaggtcaggg tcaggagccc ccccctgaac ccaggataac cctcaaagtc ggggggcaac ccgtcacctt cctggtagat actggggccc aacactccgt gctgacccaa aatcctggac ccctaagtga taagtctgcc tgggtccaag gggctactgg aggaaagcgg tatcgctgga ccacggatcg caaagtacat ctagctaccg gtaaggtcac ccactctttc ctccatgtac cagactgtcc ctatcctctg ttaggaagag atttgctgac taaactaaaa gcccaaatcc actttgaggg atcaggagcc caggttatgg gaccaatggg gcagcccctg caagtgttga ccctaaatat agaagatgag catcggctac atgagacctc aaaagagcca gatgtttctc tagggtccac atggctgtct gattttcctc aggcctgggc ggaaaccggg ggcatgggac tggcagttcg ccaagctcct ctgatcatac ctctgaaagc aacctctacc cccgtgtcca taaaacaata ccccatgtca caagaagcca gactggggat caagccccac atacagagac tgttggacca gggaatactg gtaccctgcc agtccccctg gaacacgccc ctgctacccg ttaagaaacc agggactaat gattataggc ctgtccagga tctgagagaa gtcaacaagc gggtggaaga catccacccc accgtgccca acccttacaa cctcttgagc gggctcccac cgtcccacca gtggtacact gtgcttgatt taaaggatgc ctttttctgc ctgagactcc accccaccag tcagcctctc ttcgcctttg agtggagaga tccagagatg ggaatctcag gacaattgac ctggaccaga ctcccacagg gtttcaaaaa cagtcccacc ctgtttgatg aggcactgca cagagaccta gcagacttcc ggatccagca cccagacttg atcctgctac agtacgtgga tgacttactg ctggccgcca cttctgagct agactgccaa caaggtactc gggccctgtt acaaacccta gggaacctcg ggtatcgggc ctcggccaag aaagcccaaa tttgccagaa acaggtcaag tatctggggt atcttctaaa agagggtcag agatggctga ctgaggccag aaaagagact gtgatggggc agcctactcc gaagacccct cgacaactaa gggagttcct agggacggca ggcttctgtc gcctctggat ccctgggttt gcagaaatgg cagccccctt gtaccctctc accaaaacgg ggactctgtt taattggggc ccagaccaac aaaaggccta tcaagaaatc aagcaagctc ttctaactgc cccagccctg gggttgccag atttgactaa gccctttgaa ctctttgtcg acgagaagca gggctacgcc aaaggtgtcc taacgcaaaa actgggacct tggcgtcggc cggtggccta cctgtccaaa aagctagacc cagtagcagc tgggtggccc ccttgcctac ggatggtagc agccattgcc gtactgacaa aggatgcagg caagctaacc atgggacagc cactagtcat tctggccccc catgcagtag aggcactagt caaacaaccc cccgaccgct ggctttccaa cgcccggatg actcactatc aggccttgct tttggacacg gaccgggtcc agttcggacc ggtggtagcc ctgaacccgg ctacgctgct cccactgcct gaggaagggc tgcaacacaa ctgccttgat atcctggccg aagcccacgg aacccgaccc gacctaacgg accagccgct cccagacgcc gaccacacct ggtacacgga tggaagcagt ctcttacaag agggacagcg taaggcggga gctgcggtga ccaccgagac cgaggtaatc tgggctaaag ccctgccagc cgggacatcc gctcagcggg ctgaactgat agcactcacc caggccctaa agatggcaga aggtaagaag ctaaatgttt atactgatag ccgttatgct tttgctactg cccatatcca tggagaaata tacagaaggc gtgggttgct cacatcagaa ggcaaagaga tcaaaaataa agacgagatc ttggccctac taaaagccct ctttctgccc aaaagactta gcataatcca ttgtccagga catcaaaagg gacacagcgc cgaggctaga ggcaaccgga tggctgacca agcggcccga aaggcagcca tcacagagac tccagacacc tctaccctcc tcatagaaaa ttcatcaccc tacacctcag aacattttca ttacacagtg actgatataa aggacctaac caagttgggg gccatttatg ataaaacaaa gaagtattgg gtctaccaag gaaaacctgt gatgcctgac cagtttactt ttgaattatt agactttctt catcagctga ctcacctcag cttctcaaaa atgaaggctc tcctagagag aagccacagt ccctactaca tgctgaaccg ggatcgaaca ctcaaaaata tcactgagac ctgcaaagct tgtgcacaag tcaacgccag caagtctgcc gttaaacagg gaactagggt ccgcgggcat cggcccggca ctcattggga gatcgatttc accgagataa agcccggatt gtatggctat aaatatcttc tagtttttat agataccttt tctggctgga tagaagcctt cccaaccaag aaagaaaccg ccaaggtcgt aaccaagaag ctactagagg agatcttccc caggttcggc atgcctcagg tattgggaac tgacaatggg cctgccttcg tctccaaggt gagtcagaca gtggccgatc tgttggggat tgattggaaa ttacattgtg catacagacc ccaaagctca ggccaggtag aaagaatgaa tagaaccatc aaggagactt taactaaatt aacgcttgca actggctcta gagactgggt gctcctactc cccttagccc tgtaccgagc ccgcaacacg ccgggccccc atggcctcac cccatatgag atcttatatg gggcaccccc gccccttgta aacttccctg accctgacat gacaagagtt actaacagcc cctctctcca agctcactta caggctctct acttagtcca gcacgaagtc tggagacctc tggcggcagc ctaccaagaa caactggacc gaccggtggt acctcaccct taccgagtcg gcgacacagt gtgggtccgc cgacaccaga ctaagaacct agaacctcgc tggaaaggac cttacacagt cctgctgacc acccccaccg ccctcaaagt agacggcatc gcagcttgga tacacgccgc ccacgtgaag gctgccgacc ccgggggtgg accatcctct agactgacat ggcgcgttca acgctctcaa aaccccctca agataagatt aacccgtgga agcccttaat agtcatggga gtcctgttag gagtagggat ggcagagagc ccccatcagg tctttaatgt aacctggaga gtcaccaacc tgatgactgg gcgtaccgcc aatgccacct ccctcctggg aactgtacaa gatgccttcc caaaattata ttttgatcta tgtgatctgg tcggagagga gtgggaccct tcagaccagg aaccgtatgt cgggtatggc tgcaagtacc ccgcagggag acagcggacc cggacttttg acttttacgt gtgccctggg cataccgtaa agtcggggtg tgggggacca ggagagggct actgtggtaa atgggggtgt gaaaccaccg gacaggctta ctggaagccc acatcatcgt gggacctaat ctcccttaag cgcggtaaca ccccctggga cacgggatgc tctaaagttg cctgtggccc ctgctacgac ctctccaaag tatccaattc cttccaaggg gctactcgag ggggcagatg caaccctcta gtcctagaat tcactgatgc aggaaaaaag gctaactggg acgggcccaa atcgtgggga ctgagactgt accggacagg aacagatcct attaccatgt tctccctgac ccggcaggtc cttaatgtgg gaccccgagt ccccataggg cccaacccag tattacccga ccaaagactc ccttcctcac caatagagat tgtaccggct ccacagccac ctagccccct caataccagt tacccccctt ccactaccag tacaccctca acctccccta caagtccaag tgtcccacag ccacccccag gaactggaga tagactacta gctctagtca aaggagccta tcaggcgctt aacctcacca atcccgacaa gacccaagaa tgttggctgt gcttagtgtc gggacctcct tattacgaag gagtagcggt cgtgggcact tataccaatc attccaccgc tccggccaac tgtacggcca cttcccaaca taagcttacc ctatctgaag tgacaggaca gggcctatgc atgggggcag tacctaaaac tcaccaggcc ttatgtaaca ccacccaaag cgccggctca ggatcctact accttgcagc acccgccgga acaatgtggg cttgcagcac tggattgact ccctgcttgt ccaccacggt gctcaatcta accacagatt attgtgtatt agttgaactc tggcccagag taatttacca ctcccccgat tatatgtatg gtcagcttga acagcgtacc aaatataaaa gagagccagt atcattgacc ctggcccttc tactaggagg attaaccatg ggagggattg cagctggaat agggacgggg accactgcct taattaaaac ccagcagttt gagcagcttc atgccgctat ccagacagac ctcaacgaag tcgaaaagtc aattaccaac ctagaaaagt cactgacctc gttgtctgaa gtagtcctac agaaccgcag aggcctagat ttgctattcc taaaggaggg aggtctctgc gcagccctaa aagaagaatg ttgtttttat gcagaccaca cggggctagt gagagacagc atggccaaat taagagaaag gcttaatcag agacaaaaac tatttgagac aggccaagga tggttcgaag ggctgtttaa tagatccccc tggtttacca ccttaatctc caccatcatg ggacctctaa tagtactctt actgatctta ctctttggac cttgcattct caatcgattg gtccaatttg ttaaagacag gatctcagtg gtccaggctc tggttttgac tcagcaatat caccagctaa aacccataga gtacgagcca tgaacgcgtt actggccgaa gccgcttgga ataaggccgg tgtgcgtttg tctatatgtt attttccacc atattgccgt cttttggcaa tgtgagggcc cggaaacctg gccctgtctt cttgacgagc attcctaggg gtctttcccc tctcgccaaa ggaatgcaag gtctgttgaa tgtcgtgaag gaagcagttc ctctggaagc ttcttgaaga caaacaacgt ctgtagcgac cctttgcagg cagcggaacc ccccacctgg cgacaggtgc ctctgcggcc aaaagccacg tgtataagat acacctgcaa aggcggcaca accccagtgc cacgttgtga gttggatagt tgtggaaaga gtcaaatggc tctcctcaag cgtattcaac aaggggctga aggatgccca gaaggtaccc cattgtatgg gatctgatct ggggcctcgg tgcacatgct ttacatgtgt ttagtcgagg ttaaaaaaac gtctaggccc cccgaaccac ggggacgtgg ttttcctttg aaaaacacga ttataaatgg tgaccggcgg catggcctcc aagtgggatc aaaagggcat ggatatcgct tacgaggagg ccctgctggg ctacaaggag ggcggcgtgc ctatcggcgg ctgtctgatc aacaacaagg acggcagtgt gctgggcagg ggccacaaca tgaggttcca gaagggctcc gccaccctgc acggcgagat ctccaccctg gagaactgtg gcaggctgga gggcaaggtg tacaaggaca ccaccctgta caccaccctg tccccttgtg acatgtgtac cggcgctatc atcatgtacg gcatccctag gtgtgtgatc ggcgagaacg tgaacttcaa gtccaagggc gagaagtacc tgcaaaccag gggccacgag gtggtggttg ttgacgatga gaggtgtaag aagctgatga agcagttcat cgacgagagg cctcaggact ggttcgagga tatcggcgag taagcggccg cagataaaat aaaagatttt atttagtctc cagaaaaagg ggggaatgaa agaccccacc tgtaggtttg gcaagctagc ttaagtaacg ccattttgca aggcatggaa aaatacataa ctgagaatag agaagttcag atcaaggtca ggaacagatg gaacagctga atatgggcca aacaggatat ctgtggtaag cagttcctgc cccggctcag ggccaagaac agatggaaca gctgaatatg ggccaaacag gatatctgtg gtaagcagtt cctgccccgg ctcagggcca agaacagatg gtccccagat gcggtccagc cctcagcagt ttctagagaa ccatcagatg tttccagggt gccccaagga cctgaaatga ccctgtgcct tatttgaact aaccaatcag ttcgcttctc gcttctgttc gcgcgcttct gctccccgag ctcaataaaa gagcccacaa cccctcactc ggggcgccag tcctccgatt gactgagtcg cccgggtacc cgtgtatcca ataaaccctc ttgcagttgc atccgacttg tggtctcgct gttccttggg agggtctcct ctgagtgatt gactacccgt cagcgggggt ctttcattac atgtgagcaa aaggccagca aaaggccagg aaccgtaaaa aggccgcgtt gctggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag tcagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcaatgctc acgctgtagg tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac gacttatcgc cactggcagc agccactggt aacaggatta gcagagcgag gtatgtaggc ggtgctacag agttcttgaa gtggtggcct aactacggct acactagaag gacagtattt ggtatctgcg ctctgctgaa gccagttacc ttcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga agatcctttg atcttttcta cggggtctga cgctcagtgg aacgaaaact cacgttaagg gattttggtc atgagattat caaaaaggat cttcacctag atccttttaa attaaaaatg aagttttaaa tcaatctaaa gtatatatga gtaaacttgg tctgacagtt accaatgctt aatcagtgag gcacctatct cagcgatctg tctatttcgt tcatccatag ttgcctgact ccccgtcgtg tagataacta cgatacggga gggcttacca tctggcccca gtgctgcaat gataccgcga gacccacgct caccggctcc agatttatca gcaataaacc agccagccgg aagggccgag cgcagaagtg gtcctgcaac tttatccgcc tccatccagt ctattaattg ttgccgggaa gctagagtaa gtagttcgcc agttaatagt ttgcgcaacg ttgttgccat tgctgcaggc atcgtggtgt cacgctcgtc gtttggtatg gcttcattca gctccggttc ccaacgatca aggcgagtta catgatcccc catgttgtgc aaaaaagcgg ttagctcctt cggtcctccg atcgttgtca gaagtaagtt ggccgcagtg ttatcactca tggttatggc agcactgcat aattctctta ctgtcatgcc atccgtaaga tgcttttctg tgactggtga gtactcaacc aagtcattct gagaatagtg tatgcggcga ccgagttgct cttgcccggc gtcaacacgg gataataccg cgccacatag cagaacttta aaagtgctca tcattggaaa acgttcttcg gggcgaaaac tctcaaggat cttaccgctg ttgagatcca gttcgatgta acccactcgt gcacccaact gatcttcagc atcttttact ttcaccagcg tttctgggtg agcaaaaaca ggaaggcaaa atgccgcaaa aaagggaata agggcgacac ggaaatgttg aatactcata ctcttccttt ttcaatatta ttgaagcatt tatcagggtt attgtctcat gagcggatac atatttgaat gtatttagaa aaataaacaa ataggggttc cgcgcacatt tccccgaaaa gtgccacctg acgtctaaga aaccattatt atcatgacat taacctataa aaataggcgt atcacgaggc cctttcgtct tcaagaattc at RCR Vector - pAC-yCD tagttattaa tagtaatcaa ttacggggtc attagttcat agcccatata tggagttccg cgttacataa cttacggtaa atggcccgcc tggctgaccg cccaacgacc cccgcccatt gacgtcaata atgacgtatg ttcccatagt aacgccaata gggactttcc attgacgtca atgggtggag tatttacggt aaactgccca cttggcagta catcaagtgt atcatatgcc aagtacgccc cctattgacg tcaatgacgg taaatggccc gcctggcatt atgcccagta catgacctta tgggactttc ctacttggca gtacatctac gtattagtca tcgctattac catggtgatg cggttttggc agtacatcaa tgggcgtgga tagcggtttg actcacgggg atttccaagt ctccacccca ttgacgtcaa tgggagtttg ttttggcacc aaaatcaacg ggactttcca aaatgtcgta acaactccgc cccattgacg caaatgggcg gtaggcgtgt acggtgggag gtctatataa gcagagctgg tttagtgaac cggcgccagt cctccgattg actgagtcgc ccgggtaccc gtgtatccaa taaaccctct tgcagttgca tccgacttgt ggtctcgctg ttccttggga gggtctcctc tgagtgattg actacccgtc agcgggggtc tttcatttgg gggctcgtcc gggatcggga gacccctgcc cagggaccac cgacccacca ccgggaggta agctggccag caacttatct gtgtctgtcc gattgtctag tgtctatgac tgattttatg cgcctgcgtc ggtactagtt agctaactag ctctgtatct ggcggacccg tggtggaact gacgagttcg gaacacccgg ccgcaaccct gggagacgtc ccagggactt cgggggccgt ttttgtggcc cgacctgagt ccaaaaatcc cgatcgtttt ggactctttg gtgcaccccc cttagaggag ggatatgtgg ttctggtagg agacgagaac ctaaaacagt tcccgcctcc gtctgaattt ttgctttcgg tttgggaccg aagccgcgcc gcgcgtcttg tctgctgcag catcgttctg tgttgtctct gtctgactgt gtttctgtat ttgtctgaga atatgggcca gactgttacc actcccttaa gtttgacctt aggtcactgg aaagatgtcg agcggatcgc tcacaaccag tcggtagatg tcaagaagag acgttgggtt accttctgct ctgcagaatg gccaaccttt aacgtcggat ggccgcgaga cggcaccttt aaccgagacc tcatcaccca ggttaagatc aaggtctttt cacctggccc gcatggacac ccagaccagg tcccctacat cgtgacctgg gaagccttgg cttttgaccc ccctccctgg gtcaagccct ttgtacaccc taagcctccg cctcctcttc ctccatccgc cccgtctctc ccccttgaac ctcctcgttc gaccccgcct cgatcctccc tttatccagc cctcactcct tctctaggcg ccaaacctaa acctcaagtt ctttctgaca gtggggggcc gctcatcgac ctacttacag aagacccccc gccttatagg gacccaagac cacccccttc cgacagggac ggaaatggtg gagaagcgac ccctgcggga gaggcaccgg acccctcccc aatggcatct cgcctacgtg ggagacggga gccccctgtg gccgactcca ctacctcgca ggcattcccc ctccgcgcag gaggaaacgg acagcttcaa tactggccgt tctcctcttc tgacctttac aactggaaaa ataataaccc ttctttttct gaagatccag gtaaactgac agctctgatc gagtctgttc tcatcaccca tcagcccacc tgggacgact gtcagcagct gttggggact ctgctgaccg gagaagaaaa acaacgggtg ctcttagagg ctagaaaggc ggtgcggggc gatgatgggc gccccactca actgcccaat gaagtcgatg ccgcttttcc cctcgagcgc ccagactggg attacaccac ccaggcaggt aggaaccacc tagtccacta tcgccagttg ctcctagcgg gtctccaaaa cgcgggcaga agccccacca atttggccaa ggtaaaagga ataacacaag ggcccaatga gtctccctcg gccttcctag agagacttaa ggaagcctat cgcaggtaca ctccttatga ccctgaggac ccagggcaag aaactaatgt gtctatgtct ttcatttggc agtctgcccc agacattggg agaaagttag agaggttaga agatttaaaa aacaagacgc ttggagattt ggttagagag gcagaaaaga tctttaataa acgagaaacc ccggaagaaa gagaggaacg tatcaggaga gaaacagagg aaaaagaaga acgccgtagg acagaggatg agcagaaaga gaaagaaaga gatcgtagga gacatagaga gatgagcaag ctattggcca ctgtcgttag tggacagaaa caggatagac agggaggaga acgaaggagg tcccaactcg atcgcgacca gtgtgcctac tgcaaagaaa aggggcactg ggctaaagat tgtcccaaga aaccacgagg acctcgggga ccaagacccc agacctccct cctgacccta gatgactagg gaggtcaggg tcaggagccc ccccctgaac ccaggataac cctcaaagtc ggggggcaac ccgtcacctt cctggtagat actggggccc aacactccgt gctgacccaa aatcctggac ccctaagtga taagtctgcc tgggtccaag gggctactgg aggaaagcgg tatcgctgga ccacggatcg caaagtacat ctagctaccg gtaaggtcac ccactctttc ctccatgtac cagactgtcc ctatcctctg ttaggaagag atttgctgac taaactaaaa gcccaaatcc actttgaggg atcaggagcc caggttatgg gaccaatggg gcagcccctg caagtgttga ccctaaatat agaagatgag catcggctac atgagacctc aaaagagcca gatgtttctc tagggtccac atggctgtct gattttcctc aggcctgggc ggaaaccggg ggcatgggac tggcagttcg ccaagctcct ctgatcatac ctctgaaagc aacctctacc cccgtgtcca taaaacaata ccccatgtca caagaagcca gactggggat caagccccac atacagagac tgttggacca gggaatactg gtaccctgcc agtccccctg gaacacgccc ctgctacccg ttaagaaacc agggactaat gattataggc ctgtccagga tctgagagaa gtcaacaagc gggtggaaga catccacccc accgtgccca acccttacaa cctcttgagc gggctcccac cgtcccacca gtggtacact gtgcttgatt taaaggatgc ctttttctgc ctgagactcc accccaccag tcagcctctc ttcgcctttg agtggagaga tccagagatg ggaatctcag gacaattgac ctggaccaga ctcccacagg gtttcaaaaa cagtcccacc ctgtttgatg aggcactgca cagagaccta gcagacttcc ggatccagca cccagacttg atcctgctac agtacgtgga tgacttactg ctggccgcca cttctgagct agactgccaa caaggtactc gggccctgtt acaaacccta gggaacctcg ggtatcgggc ctcggccaag aaagcccaaa tttgccagaa acaggtcaag tatctggggt atcttctaaa agagggtcag agatggctga ctgaggccag aaaagagact gtgatggggc agcctactcc gaagacccct cgacaactaa gggagttcct agggacggca ggcttctgtc gcctctggat ccctgggttt gcagaaatgg cagccccctt gtaccctctc accaaaacgg ggactctgtt taattggggc ccagaccaac aaaaggccta tcaagaaatc aagcaagctc ttctaactgc cccagccctg gggttgccag atttgactaa gccctttgaa ctctttgtcg acgagaagca gggctacgcc aaaggtgtcc taacgcaaaa actgggacct tggcgtcggc cggtggccta cctgtccaaa aagctagacc cagtagcagc tgggtggccc ccttgcctac ggatggtagc agccattgcc gtactgacaa aggatgcagg caagctaacc atgggacagc cactagtcat tctggccccc catgcagtag aggcactagt caaacaaccc cccgaccgct ggctttccaa cgcccggatg actcactatc aggccttgct tttggacacg gaccgggtcc agttcggacc ggtggtagcc ctgaacccgg ctacgctgct cccactgcct gaggaagggc tgcaacacaa ctgccttgat atcctggccg aagcccacgg aacccgaccc gacctaacgg accagccgct cccagacgcc gaccacacct ggtacacgga tggaagcagt ctcttacaag agggacagcg taaggcggga gctgcggtga ccaccgagac cgaggtaatc tgggctaaag ccctgccagc cgggacatcc gctcagcggg ctgaactgat agcactcacc caggccctaa agatggcaga aggtaagaag ctaaatgttt atactgatag ccgttatgct tttgctactg cccatatcca tggagaaata tacagaaggc gtgggttgct cacatcagaa ggcaaagaga tcaaaaataa agacgagatc ttggccctac taaaagccct ctttctgccc aaaagactta gcataatcca ttgtccagga catcaaaagg gacacagcgc cgaggctaga ggcaaccgga tggctgacca agcggcccga aaggcagcca tcacagagac tccagacacc tctaccctcc tcatagaaaa ttcatcaccc tacacctcag aacattttca ttacacagtg actgatataa aggacctaac caagttgggg gccatttatg ataaaacaaa gaagtattgg gtctaccaag gaaaacctgt gatgcctgac cagtttactt ttgaattatt agactttctt catcagctga ctcacctcag cttctcaaaa atgaaggctc tcctagagag aagccacagt ccctactaca tgctgaaccg ggatcgaaca ctcaaaaata tcactgagac ctgcaaagct tgtgcacaag tcaacgccag caagtctgcc gttaaacagg gaactagggt ccgcgggcat cggcccggca ctcattggga gatcgatttc accgagataa agcccggatt gtatggctat aaatatcttc tagtttttat agataccttt tctggctgga tagaagcctt cccaaccaag aaagaaaccg ccaaggtcgt aaccaagaag ctactagagg agatcttccc caggttcggc atgcctcagg tattgggaac tgacaatggg cctgccttcg tctccaaggt gagtcagaca gtggccgatc tgttggggat tgattggaaa ttacattgtg catacagacc ccaaagctca ggccaggtag aaagaatgaa tagaaccatc aaggagactt taactaaatt aacgcttgca actggctcta gagactgggt gctcctactc cccttagccc tgtaccgagc ccgcaacacg ccgggccccc atggcctcac cccatatgag atcttatatg gggcaccccc gccccttgta aacttccctg accctgacat gacaagagtt actaacagcc cctctctcca agctcactta caggctctct acttagtcca gcacgaagtc tggagacctc tggcggcagc ctaccaagaa caactggacc gaccggtggt acctcaccct taccgagtcg gcgacacagt gtgggtccgc cgacaccaga ctaagaacct agaacctcgc tggaaaggac cttacacagt cctgctgacc acccccaccg ccctcaaagt agacggcatc gcagcttgga tacacgccgc ccacgtgaag gctgccgacc ccgggggtgg accatcctct agactgacat ggcgcgttca acgctctcaa aaccccctca agataagatt aacccgtgga agcccttaat agtcatggga gtcctgttag gagtagggat ggcagagagc ccccatcagg tctttaatgt aacctggaga gtcaccaacc tgatgactgg gcgtaccgcc aatgccacct ccctcctggg aactgtacaa gatgccttcc caaaattata ttttgatcta tgtgatctgg tcggagagga gtgggaccct tcagaccagg aaccgtatgt cgggtatggc tgcaagtacc ccgcagggag acagcggacc cggacttttg acttttacgt gtgccctggg cataccgtaa agtcggggtg tgggggacca ggagagggct actgtggtaa atgggggtgt gaaaccaccg gacaggctta ctggaagccc acatcatcgt gggacctaat ctcccttaag cgcggtaaca ccccctggga cacgggatgc tctaaagttg cctgtggccc ctgctacgac ctctccaaag tatccaattc cttccaaggg gctactcgag ggggcagatg caaccctcta gtcctagaat tcactgatgc aggaaaaaag gctaactggg acgggcccaa atcgtgggga ctgagactgt accggacagg aacagatcct attaccatgt tctccctgac ccggcaggtc cttaatgtgg gaccccgagt ccccataggg cccaacccag tattacccga ccaaagactc ccttcctcac caatagagat tgtaccggct ccacagccac ctagccccct caataccagt tacccccctt ccactaccag tacaccctca acctccccta caagtccaag tgtcccacag ccacccccag gaactggaga tagactacta gctctagtca aaggagccta tcaggcgctt aacctcacca atcccgacaa gacccaagaa tgttggctgt gcttagtgtc gggacctcct tattacgaag gagtagcggt cgtgggcact tataccaatc attccaccgc tccggccaac tgtacggcca cttcccaaca taagcttacc ctatctgaag tgacaggaca gggcctatgc atgggggcag tacctaaaac tcaccaggcc ttatgtaaca ccacccaaag cgccggctca ggatcctact accttgcagc acccgccgga acaatgtggg cttgcagcac tggattgact ccctgcttgt ccaccacggt gctcaatcta accacagatt attgtgtatt agttgaactc tggcccagag taatttacca ctcccccgat tatatgtatg gtcagcttga acagcgtacc aaatataaaa gagagccagt atcattgacc ctggcccttc tactaggagg attaaccatg ggagggattg cagctggaat agggacgggg accactgcct taattaaaac ccagcagttt gagcagcttc atgccgctat ccagacagac ctcaacgaag tcgaaaagtc aattaccaac ctagaaaagt cactgacctc gttgtctgaa gtagtcctac agaaccgcag aggcctagat ttgctattcc taaaggaggg aggtctctgc gcagccctaa aagaagaatg ttgtttttat gcagaccaca cggggctagt gagagacagc atggccaaat taagagaaag gcttaatcag agacaaaaac tatttgagac aggccaagga tggttcgaag ggctgtttaa tagatccccc tggtttacca ccttaatctc caccatcatg ggacctctaa tagtactctt actgatctta ctctttggac cttgcattct caatcgattg gtccaatttg ttaaagacag gatctcagtg gtccaggctc tggttttgac tcagcaatat caccagctaa aacccataga gtacgagcca tgaacgcgtt actggccgaa gccgcttgga ataaggccgg tgtgcgtttg tctatatgtt attttccacc atattgccgt cttttggcaa tgtgagggcc cggaaacctg gccctgtctt cttgacgagc attcctaggg gtctttcccc tctcgccaaa ggaatgcaag gtctgttgaa tgtcgtgaag gaagcagttc ctctggaagc ttcttgaaga caaacaacgt ctgtagcgac cctttgcagg cagcggaacc ccccacctgg cgacaggtgc ctctgcggcc aaaagccacg tgtataagat acacctgcaa aggcggcaca accccagtgc cacgttgtga gttggatagt tgtggaaaga gtcaaatggc tctcctcaag cgtattcaac aaggggctga aggatgccca gaaggtaccc cattgtatgg gatctgatct ggggcctcgg tgcacatgct ttacatgtgt ttagtcgagg ttaaaaaaac gtctaggccc cccgaaccac ggggacgtgg ttttcctttg aaaaacacga ttataaatgg tgacaggggg aatggcaagc aagtgggatc agaagggtat ggacattgcc tatgaggagg cggccttagg ttacaaagag ggtggtgttc ctattggcgg atgtcttatc aataacaaag acggaagtgt tctcggtcgt ggtcacaaca tgagatttca aaagggatcc gccacactac atggtgagat ctccactttg gaaaactgtg ggagattaga gggcaaagtg tacaaagata ccactttgta tacgacgctg tctccatgcg acatgtgtac aggtgccatc atcatgtatg gtattccacg ctgtgttgtc ggtgagaacg ttaatttcaa aagtaagggc gagaaatatt tacaaactag aggtcacgag gttgttgttg ttgacgatga gaggtgtaaa aagatcatga aacaatttat cgatgaaaga cctcaggatt ggtttgaaga tattggtgag taggcggccg cagataaaat aaaagatttt atttagtctc cagaaaaagg ggggaatgaa agaccccacc tgtaggtttg gcaagctagc ttaagtaacg ccattttgca aggcatggaa aaatacataa ctgagaatag agaagttcag atcaaggtca ggaacagatg gaacagctga atatgggcca aacaggatat ctgtggtaag cagttcctgc cccggctcag ggccaagaac agatggaaca gctgaatatg ggccaaacag gatatctgtg gtaagcagtt cctgccccgg ctcagggcca agaacagatg gtccccagat gcggtccagc cctcagcagt ttctagagaa ccatcagatg tttccagggt gccccaagga cctgaaatga ccctgtgcct tatttgaact aaccaatcag ttcgcttctc gcttctgttc gcgcgcttct gctccccgag ctcaataaaa gagcccacaa cccctcactc ggggcgccag tcctccgatt gactgagtcg cccgggtacc cgtgtatcca ataaaccctc ttgcagttgc atccgacttg tggtctcgct gttccttggg agggtctcct ctgagtgatt gactacccgt cagcgggggt ctttcattac atgtgagcaa aaggccagca aaaggccagg aaccgtaaaa aggccgcgtt gctggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag tcagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcaatgctc acgctgtagg tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac gacttatcgc cactggcagc agccactggt aacaggatta gcagagcgag gtatgtaggc ggtgctacag agttcttgaa gtggtggcct aactacggct acactagaag gacagtattt ggtatctgcg ctctgctgaa gccagttacc ttcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga agatcctttg atcttttcta cggggtctga cgctcagtgg aacgaaaact cacgttaagg gattttggtc atgagattat caaaaaggat cttcacctag atccttttaa attaaaaatg aagttttaaa tcaatctaaa gtatatatga gtaaacttgg tctgacagtt accaatgctt aatcagtgag gcacctatct cagcgatctg tctatttcgt tcatccatag ttgcctgact ccccgtcgtg tagataacta cgatacggga gggcttacca tctggcccca gtgctgcaat gataccgcga gacccacgct caccggctcc agatttatca gcaataaacc agccagccgg aagggccgag cgcagaagtg gtcctgcaac tttatccgcc tccatccagt ctattaattg ttgccgggaa gctagagtaa gtagttcgcc agttaatagt ttgcgcaacg ttgttgccat tgctgcaggc atcgtggtgt cacgctcgtc gtttggtatg gcttcattca gctccggttc ccaacgatca aggcgagtta catgatcccc catgttgtgc aaaaaagcgg ttagctcctt cggtcctccg atcgttgtca gaagtaagtt ggccgcagtg ttatcactca tggttatggc agcactgcat aattctctta ctgtcatgcc atccgtaaga tgcttttctg tgactggtga gtactcaacc aagtcattct gagaatagtg tatgcggcga ccgagttgct cttgcccggc gtcaacacgg gataataccg cgccacatag cagaacttta aaagtgctca tcattggaaa acgttcttcg gggcgaaaac tctcaaggat cttaccgctg ttgagatcca gttcgatgta acccactcgt gcacccaact gatcttcagc atcttttact ttcaccagcg tttctgggtg agcaaaaaca ggaaggcaaa atgccgcaaa aaagggaata agggcgacac ggaaatgttg aatactcata ctcttccttt ttcaatatta ttgaagcatt tatcagggtt attgtctcat gagcggatac atatttgaat gtatttagaa aaataaacaa ataggggttc cgcgcacatt tccccgaaaa gtgccacctg acgtctaaga aaccattatt atcatgacat taacctataa aaataggcgt atcacgaggc cctttcgtct tcaagaattc at RCR Vector - pACE-CD tagttattaa tagtaatcaa ttacggggtc attagttcat agcccatata tggagttccg cgttacataa cttacggtaa atggcccgcc tggctgaccg cccaacgacc cccgcccatt gacgtcaata atgacgtatg ttcccatagt aacgccaata gggactttcc attgacgtca atgggtggag tatttacggt aaactgccca cttggcagta catcaagtgt atcatatgcc aagtacgccc cctattgacg tcaatgacgg taaatggccc gcctggcatt atgcccagta catgacctta tgggactttc ctacttggca gtacatctac gtattagtca tcgctattac catggtgatg cggttttggc agtacatcaa tgggcgtgga tagcggtttg actcacgggg atttccaagt ctccacccca ttgacgtcaa tgggagtttg ttttggcacc aaaatcaacg ggactttcca aaatgtcgta acaactccgc cccattgacg caaatgggcg gtaggcgtgt acggtgggag gtctatataa gcagagctgg tttagtgaac cggcgccagt cctccgattg actgagtcgc ccgggtaccc gtgtatccaa taaaccctct tgcagttgca tccgacttgt ggtctcgctg ttccttggga gggtctcctc tgagtgattg actacccgtc agcgggggtc tttcatttgg gggctcgtcc gggatcggga gacccctgcc cagggaccac cgacccacca ccgggaggta agctggccag caacttatct gtgtctgtcc gattgtctag tgtctatgac tgattttatg cgcctgcgtc ggtactagtt agctaactag ctctgtatct ggcggacccg tggtggaact gacgagttcg gaacacccgg ccgcaaccct gggagacgtc ccagggactt cgggggccgt ttttgtggcc cgacctgagt ccaaaaatcc cgatcgtttt ggactctttg gtgcaccccc cttagaggag ggatatgtgg ttctggtagg agacgagaac ctaaaacagt tcccgcctcc gtctgaattt ttgctttcgg tttgggaccg aagccgcgcc gcgcgtcttg tctgctgcag catcgttctg tgttgtctct gtctgactgt gtttctgtat ttgtctgaga atatgggcca gactgttacc actcccttaa gtttgacctt aggtcactgg aaagatgtcg agcggatcgc tcacaaccag tcggtagatg tcaagaagag acgttgggtt accttctgct ctgcagaatg gccaaccttt aacgtcggat ggccgcgaga cggcaccttt aaccgagacc tcatcaccca ggttaagatc aaggtctttt cacctggccc gcatggacac ccagaccagg tcccctacat cgtgacctgg gaagccttgg cttttgaccc ccctccctgg gtcaagccct ttgtacaccc taagcctccg cctcctcttc ctccatccgc cccgtctctc ccccttgaac ctcctcgttc gaccccgcct cgatcctccc tttatccagc cctcactcct tctctaggcg ccaaacctaa acctcaagtt ctttctgaca gtggggggcc gctcatcgac ctacttacag aagacccccc gccttatagg gacccaagac cacccccttc cgacagggac ggaaatggtg gagaagcgac ccctgcggga gaggcaccgg acccctcccc aatggcatct cgcctacgtg ggagacggga gccccctgtg gccgactcca ctacctcgca ggcattcccc ctccgcgcag gaggaaacgg acagcttcaa tactggccgt tctcctcttc tgacctttac aactggaaaa ataataaccc ttctttttct gaagatccag gtaaactgac agctctgatc gagtctgttc tcatcaccca tcagcccacc tgggacgact gtcagcagct gttggggact ctgctgaccg gagaagaaaa acaacgggtg ctcttagagg ctagaaaggc ggtgcggggc gatgatgggc gccccactca actgcccaat gaagtcgatg ccgcttttcc cctcgagcgc ccagactggg attacaccac ccaggcaggt aggaaccacc tagtccacta tcgccagttg ctcctagcgg gtctccaaaa cgcgggcaga agccccacca atttggccaa ggtaaaagga ataacacaag ggcccaatga gtctccctcg gccttcctag agagacttaa ggaagcctat cgcaggtaca ctccttatga ccctgaggac ccagggcaag aaactaatgt gtctatgtct ttcatttggc agtctgcccc agacattggg agaaagttag agaggttaga agatttaaaa aacaagacgc ttggagattt ggttagagag gcagaaaaga tctttaataa acgagaaacc ccggaagaaa gagaggaacg tatcaggaga gaaacagagg aaaaagaaga acgccgtagg acagaggatg agcagaaaga gaaagaaaga gatcgtagga gacatagaga gatgagcaag ctattggcca ctgtcgttag tggacagaaa caggatagac agggaggaga acgaaggagg tcccaactcg atcgcgacca gtgtgcctac tgcaaagaaa aggggcactg ggctaaagat tgtcccaaga aaccacgagg acctcgggga ccaagacccc agacctccct cctgacccta gatgactagg gaggtcaggg tcaggagccc ccccctgaac ccaggataac cctcaaagtc ggggggcaac ccgtcacctt cctggtagat actggggccc aacactccgt gctgacccaa aatcctggac ccctaagtga taagtctgcc tgggtccaag gggctactgg aggaaagcgg tatcgctgga ccacggatcg caaagtacat ctagctaccg gtaaggtcac ccactctttc ctccatgtac cagactgtcc ctatcctctg ttaggaagag atttgctgac taaactaaaa gcccaaatcc actttgaggg atcaggagcc caggttatgg gaccaatggg gcagcccctg caagtgttga ccctaaatat agaagatgag catcggctac atgagacctc aaaagagcca gatgtttctc tagggtccac atggctgtct gattttcctc aggcctgggc ggaaaccggg ggcatgggac tggcagttcg ccaagctcct ctgatcatac ctctgaaagc aacctctacc cccgtgtcca taaaacaata ccccatgtca caagaagcca gactggggat caagccccac atacagagac tgttggacca gggaatactg gtaccctgcc agtccccctg gaacacgccc ctgctacccg ttaagaaacc agggactaat gattataggc ctgtccagga tctgagagaa gtcaacaagc gggtggaaga catccacccc accgtgccca acccttacaa cctcttgagc gggctcccac cgtcccacca gtggtacact gtgcttgatt taaaggatgc ctttttctgc ctgagactcc accccaccag tcagcctctc ttcgcctttg agtggagaga tccagagatg ggaatctcag gacaattgac ctggaccaga ctcccacagg gtttcaaaaa cagtcccacc ctgtttgatg aggcactgca cagagaccta gcagacttcc ggatccagca cccagacttg atcctgctac agtacgtgga tgacttactg ctggccgcca cttctgagct agactgccaa caaggtactc gggccctgtt acaaacccta gggaacctcg ggtatcgggc ctcggccaag aaagcccaaa tttgccagaa acaggtcaag tatctggggt atcttctaaa agagggtcag agatggctga ctgaggccag aaaagagact gtgatggggc agcctactcc gaagacccct cgacaactaa gggagttcct agggacggca ggcttctgtc gcctctggat ccctgggttt gcagaaatgg cagccccctt gtaccctctc accaaaacgg ggactctgtt taattggggc ccagaccaac aaaaggccta tcaagaaatc aagcaagctc ttctaactgc cccagccctg gggttgccag atttgactaa gccctttgaa ctctttgtcg acgagaagca gggctacgcc aaaggtgtcc taacgcaaaa actgggacct tggcgtcggc cggtggccta cctgtccaaa aagctagacc cagtagcagc tgggtggccc ccttgcctac ggatggtagc agccattgcc gtactgacaa aggatgcagg caagctaacc atgggacagc cactagtcat tctggccccc catgcagtag aggcactagt caaacaaccc cccgaccgct ggctttccaa cgcccggatg actcactatc aggccttgct tttggacacg gaccgggtcc agttcggacc ggtggtagcc ctgaacccgg ctacgctgct cccactgcct gaggaagggc tgcaacacaa ctgccttgat atcctggccg aagcccacgg aacccgaccc gacctaacgg accagccgct cccagacgcc gaccacacct ggtacacgga tggaagcagt ctcttacaag agggacagcg taaggcggga gctgcggtga ccaccgagac cgaggtaatc tgggctaaag ccctgccagc cgggacatcc gctcagcggg ctgaactgat agcactcacc caggccctaa agatggcaga aggtaagaag ctaaatgttt atactgatag ccgttatgct tttgctactg cccatatcca tggagaaata tacagaaggc gtgggttgct cacatcagaa ggcaaagaga tcaaaaataa agacgagatc ttggccctac taaaagccct ctttctgccc aaaagactta gcataatcca ttgtccagga catcaaaagg gacacagcgc cgaggctaga ggcaaccgga tggctgacca agcggcccga aaggcagcca tcacagagac tccagacacc tctaccctcc tcatagaaaa ttcatcaccc tacacctcag aacattttca ttacacagtg actgatataa aggacctaac caagttgggg gccatttatg ataaaacaaa gaagtattgg gtctaccaag gaaaacctgt gatgcctgac cagtttactt ttgaattatt agactttctt catcagctga ctcacctcag cttctcaaaa atgaaggctc tcctagagag aagccacagt ccctactaca tgctgaaccg ggatcgaaca ctcaaaaata tcactgagac ctgcaaagct tgtgcacaag tcaacgccag caagtctgcc gttaaacagg gaactagggt ccgcgggcat cggcccggca ctcattggga gatcgatttc accgagataa agcccggatt gtatggctat aaatatcttc tagtttttat agataccttt tctggctgga tagaagcctt cccaaccaag aaagaaaccg ccaaggtcgt aaccaagaag ctactagagg agatcttccc caggttcggc atgcctcagg tattgggaac tgacaatggg cctgccttcg tctccaaggt gagtcagaca gtggccgatc tgttggggat tgattggaaa ttacattgtg catacagacc ccaaagctca ggccaggtag aaagaatgaa tagaaccatc aaggagactt taactaaatt aacgcttgca actggctcta gagactgggt gctcctactc cccttagccc tgtaccgagc ccgcaacacg ccgggccccc atggcctcac cccatatgag atcttatatg gggcaccccc gccccttgta aacttccctg accctgacat gacaagagtt actaacagcc cctctctcca agctcactta caggctctct acttagtcca gcacgaagtc tggagacctc tggcggcagc ctaccaagaa caactggacc gaccggtggt acctcaccct taccgagtcg gcgacacagt gtgggtccgc cgacaccaga ctaagaacct agaacctcgc tggaaaggac cttacacagt cctgctgacc acccccaccg ccctcaaagt agacggcatc gcagcttgga tacacgccgc ccacgtgaag gctgccgacc ccgggggtgg accatcctct agactgacat ggcgcgttca acgctctcaa aaccccctca agataagatt aacccgtgga agcccttaat agtcatggga gtcctgttag gagtagggat ggcagagagc ccccatcagg tctttaatgt aacctggaga gtcaccaacc tgatgactgg gcgtaccgcc aatgccacct ccctcctggg aactgtacaa gatgccttcc caaaattata ttttgatcta tgtgatctgg tcggagagga gtgggaccct tcagaccagg aaccgtatgt cgggtatggc tgcaagtacc ccgcagggag acagcggacc cggacttttg acttttacgt gtgccctggg cataccgtaa agtcggggtg tgggggacca ggagagggct actgtggtaa atgggggtgt gaaaccaccg gacaggctta ctggaagccc acatcatcgt gggacctaat ctcccttaag cgcggtaaca ccccctggga cacgggatgc tctaaagttg cctgtggccc ctgctacgac ctctccaaag tatccaattc cttccaaggg gctactcgag ggggcagatg caaccctcta gtcctagaat tcactgatgc aggaaaaaag gctaactggg acgggcccaa atcgtgggga ctgagactgt accggacagg aacagatcct attaccatgt tctccctgac ccggcaggtc cttaatgtgg gaccccgagt ccccataggg cccaacccag tattacccga ccaaagactc ccttcctcac caatagagat tgtaccggct ccacagccac ctagccccct caataccagt tacccccctt ccactaccag tacaccctca acctccccta caagtccaag tgtcccacag ccacccccag gaactggaga tagactacta gctctagtca aaggagccta tcaggcgctt aacctcacca atcccgacaa gacccaagaa tgttggctgt gcttagtgtc gggacctcct tattacgaag gagtagcggt cgtgggcact tataccaatc attccaccgc tccggccaac tgtacggcca cttcccaaca taagcttacc ctatctgaag tgacaggaca gggcctatgc atgggggcag tacctaaaac tcaccaggcc ttatgtaaca ccacccaaag cgccggctca ggatcctact accttgcagc acccgccgga acaatgtggg cttgcagcac tggattgact ccctgcttgt ccaccacggt gctcaatcta accacagatt attgtgtatt agttgaactc tggcccagag taatttacca ctcccccgat tatatgtatg gtcagcttga acagcgtacc aaatataaaa gagagccagt atcattgacc ctggcccttc tactaggagg attaaccatg ggagggattg cagctggaat agggacgggg accactgcct taattaaaac ccagcagttt gagcagcttc atgccgctat ccagacagac ctcaacgaag tcgaaaagtc aattaccaac ctagaaaagt cactgacctc gttgtctgaa gtagtcctac agaaccgcag aggcctagat ttgctattcc taaaggaggg aggtctctgc gcagccctaa aagaagaatg ttgtttttat gcagaccaca cggggctagt gagagacagc atggccaaat taagagaaag gcttaatcag agacaaaaac tatttgagac aggccaagga tggttcgaag ggctgtttaa tagatccccc tggtttacca ccttaatctc caccatcatg ggacctctaa tagtactctt actgatctta ctctttggac cttgcattct caatcgatta gtccaatttg ttaaagacag gatatcagtg gtccaggctc tagttttgac tcaacaatat caccagctga agcctataga gtacgagcca tgacgtacgt tactggccga agccgcttgg aataaggccg gtgtgcgttt gtctatatgt tattttccac catattgccg tcttttggca atgtgagggc ccggaaacct ggccctgtct tcttgacgag cattcctagg ggtctttccc ctctcgccaa aggaatgcaa ggtctgttga atgtcgtgaa ggaagcagtt cctctggaag cttcttgaag acaaacaacg tctgtagcga ccctttgcag gcagcggaac cccccacctg gcgacaggtg cctctgcggc caaaagccac gtgtataaga tacacctgca aaggcggcac aaccccagtg ccacgttgtg agttggatag ttgtggaaag agtcaaatgg ctctcctcaa gcgtattcaa caaggggctg aaggatgccc agaaggtacc ccattgtatg ggatctgatc tggggcctcg gtgcacatgc tttacatgtg tttagtcgag gttaaaaaaa cgtctaggcc ccccgaacca cggggacgtg gttttccttt gaaaaacacg ataataccat ggtgacaggg ggaatggcaa gcaagtggga tcagaagggt atggacattg cctatgagga ggcggcctta ggttacaaag agggtggtgt tcctattggc ggatgtctta tcaataacaa agacggaagt gttctcggtc gtggtcacaa catgagattt caaaagggat ccgccacact acatggtgag atctccactt tggaaaactg tgggagatta gagggcaaag tgtacaaaga taccactttg tatacgacgc tgtctccatg cgacatgtgt acaggtgcca tcatcatgta tggtattcca cgctgtgttg tcggtgagaa cgttaatttc aaaagtaagg gcgagaaata tttacaaact agaggtcacg aggttgttgt tgttgacgat gagaggtgta aaaagatcat gaaacaattt atcgatgaaa gacctcagga ttggtttgaa gatattggtg agtaggcggc cgcgccatag ataaaataaa agattttatt tagtctccag aaaaaggggg gaatgaaaga ccccacctgt aggtttggca agctagctta agtaacgcca ttttgcaagg catggaaaaa tacataactg agaatagaga agttcagatc aaggtcagga acagatggaa cagctgaata tgggccaaac aggatatctg tggtaagcag ttcctgcccc ggctcagggc caagaacaga tggaacagct gaatatgggc caaacaggat atctgtggta agcagttcct gccccggctc agggccaaga acagatggtc cccagatgcg gtccagccct cagcagtttc tagagaacca tcagatgttt ccagggtgcc ccaaggacct gaaatgaccc tgtgccttgt ttaaactaac caatcagttc gcttctcgct tctgttcgcg cgcttctgct ccccgagctc aataaaagag cccacaaccc ctcactcggg gcgccagtcc tccgattgac tgagtcgccc gggtacccgt gtatccaata aaccctcttg cagttgcatc cgacttgtgg tctcgctgtt ccttgggagg gtctcctctg agtgattgac tacccgtcag cgggggtctt tcatttgggg gctcgtccgg gatcgggaga cccctgccca gggaccaccg acccaccacc gggaggtaag ctggctgcct cgcgcgtttc ggtgatgacg gtgaaaacct ctgacatgtg agcaaaaggc cagcaaaagg ccaggaaccg taaaaaggcc gcgttgctgg cgtttttcca taggctccgc ccccctgacg agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga ctataaagat accaggcgtt tccccctgga agctccctcg tgcgctctcc tgttccgacc ctgccgctta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcaa tgctcacgct gtaggtatct cagttcggtg taggtcgttc gctccaagct gggctgtgtg cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc aacccggtaa gacacgactt atcgccactg gcagcagcca ctggtaacag gattagcaga gcgaggtatg taggcggtgc tacagagttc ttgaagtggt ggcctaacta cggctacact agaaggacag tatttggtat ctgcgctctg ctgaagccag ttaccttcgg aaaaagagtt ggtagctctt gatccggcaa acaaaccacc gctggtagcg gtggtttttt tgtttgcaag cagcagatta cgcgcagaaa aaaaggatct caagaagatc ctttgatctt ttctacgggg tctgacgctc agtggaacga aaactcacgt taagggattt tggtcatgag attatcaaaa aggatcttca cctagatcct tttaaattaa aaatgaagtt ttaaatcaat ctaaagtata tatgagtaaa cttggtctga cagttaccaa tgcttaatca gtgaggcacc tatctcagcg atctgtctat ttcgttcatc catagttgcc tgactccccg tcgtgtagat aactacgata cgggagggct taccatctgg ccccagtgct gcaatgatac cgcgagaccc acgctcaccg gctccagatt tatcagcaat aaaccagcca gccggaaggg ccgagcgcag aagtggtcct gcaactttat ccgcctccat ccagtctatt aattgttgcc gggaagctag agtaagtagt tcgccagtta atagtttgcg caacgttgtt gccattgctg caggcatcgt ggtgtcacgc tcgtcgtttg gtatggcttc attcagctcc ggttcccaac gatcaaggcg agttacatga tcccccatgt tgtgcaaaaa agcggttagc tccttcggtc ctccgatcgt tgtcagaagt aagttggccg cagtgttatc actcatggtt atggcagcac tgcataattc tcttactgtc atgccatccg taagatgctt ttctgtgact ggtgagtact caaccaagtc attctgagaa tagtgtatgc ggcgaccgag ttgctcttgc ccggcgtcaa cacgggataa taccgcgcca catagcagaa ctttaaaagt gctcatcatt ggaaaacgtt cttcggggcg aaaactctca aggatcttac cgctgttgag atccagttcg atgtaaccca ctcgtgcacc caactgatct tcagcatctt ttactttcac cagcgtttct gggtgagcaa aaacaggaag gcaaaatgcc gcaaaaaagg gaataagggc gacacggaaa tgttgaatac tcatactctt cctttttcaa tattattgaa gcatttatca gggttattgt ctcatgagcg gatacatatt tgaatgtatt tagaaaaata aacaaatagg ggttccgcgc acatttcccc gaaaagtgcc acctgacgtc taagaaacca ttattatcat gacattaacc tataaaaata ggcgtatcac gaggcccttt cgtcttcaag aattcat RCR Vector - pAC-yCD tagttattaa tagtaatcaa ttacggggtc attagttcat agcccatata tggagttccg cgttacataa cttacggtaa atggcccgcc tggctgaccg cccaacgacc cccgcccatt gacgtcaata atgacgtatg ttcccatagt aacgccaata gggactttcc attgacgtca atgggtggag tatttacggt aaactgccca cttggcagta catcaagtgt atcatatgcc aagtacgccc cctattgacg tcaatgacgg taaatggccc gcctggcatt atgcccagta catgacctta tgggactttc ctacttggca gtacatctac gtattagtca tcgctattac catggtgatg cggttttggc agtacatcaa tgggcgtgga tagcggtttg actcacgggg atttccaagt ctccacccca ttgacgtcaa tgggagtttg ttttggcacc aaaatcaacg ggactttcca aaatgtcgta acaactccgc cccattgacg caaatgggcg gtaggcgtgt acggtgggag gtctatataa gcagagctgg tttagtgaac cggcgccagt cctccgattg actgagtcgc ccgggtaccc gtgtatccaa taaaccctct tgcagttgca tccgacttgt ggtctcgctg ttccttggga gggtctcctc tgagtgattg actacccgtc agcgggggtc tttcatttgg gggctcgtcc gggatcggga gacccctgcc cagggaccac cgacccacca ccgggaggta agctggccag caacttatct gtgtctgtcc gattgtctag tgtctatgac tgattttatg cgcctgcgtc ggtactagtt agctaactag ctctgtatct ggcggacccg tggtggaact gacgagttcg gaacacccgg ccgcaaccct gggagacgtc ccagggactt cgggggccgt ttttgtggcc cgacctgagt ccaaaaatcc cgatcgtttt ggactctttg gtgcaccccc cttagaggag ggatatgtgg ttctggtagg agacgagaac ctaaaacagt tcccgcctcc gtctgaattt ttgctttcgg tttgggaccg aagccgcgcc gcgcgtcttg tctgctgcag catcgttctg tgttgtctct gtctgactgt gtttctgtat ttgtctgaaa atatgggcca gactgttacc actcccttaa gtttgacctt aggtcactgg aaagatgtcg agcggatcgc tcacaaccag tcggtagatg tcaagaagag acgttgggtt accttctgct ctgcagaatg gccaaccttt aacgtcggat ggccgcgaga cggcaccttt aaccgagacc tcatcaccca ggttaagatc aaggtctttt cacctggccc gcatggacac ccagaccagg tcccctacat cgtgacctgg gaagccttgg cttttgaccc ccctccctgg gtcaagccct ttgtacaccc taagcctccg cctcctcttc ctccatccgc cccgtctctc ccccttgaac ctcctcgttc gaccccgcct cgatcctccc tttatccagc cctcactcct tctctaggcg ccaaacctaa acctcaagtt ctttctgaca gtggggggcc gctcatcgac ctacttacag aagacccccc gccttatagg gacccaagac cacccccttc cgacagggac ggaaatggtg gagaagcgac ccctgcggga gaggcaccgg acccctcccc aatggcatct cgcctacgtg ggagacggga gccccctgtg gccgactcca ctacctcgca ggcattcccc ctccgcgcag gaggaaacgg acagcttcaa tactggccgt tctcctcttc tgacctttac aactggaaaa ataataaccc ttctttttct gaagatccag gtaaactgac agctctgatc gagtctgtcc tcatcaccca tcagcccacc tgggacgact gtcagcagct gttggggact ctgctgaccg gagaagaaaa acaacgggtg ctcttagagg ctagaaaggc ggtgcggggc gatgatgggc gccccactca actgcccaat gaagtcgatg ccgcttttcc cctcgagcgc ccagactggg attacaccac ccaggcaggt aggaaccacc tagtccacta tcgccagttg ctcctagcgg gtctccaaaa cgcgggcaga agccccacca atttggccaa ggtaaaagga ataacacaag ggcccaatga gtctccctcg gccttcctag agagacttaa ggaagcctat cgcaggtaca ctccttatga ccctgaggac ccagggcaag aaactaatgt gtctatgtct ttcatttggc agtctgcccc agacattggg agaaagttag agaggttaga agatttaaaa aacaagacgc ttggagattt ggttagagag gcagaaaaga tctttaataa acgagaaacc ccggaagaaa gagaggaacg tatcaggaga gaaacagagg aaaaagaaga acgccgtagg acagaggatg agcagaaaga gaaagaaaga gatcgtagga gacatagaga gatgagcaag ctattggcca ctgtcgttag tggacagaaa caggatagac agggaggaga acgaaggagg tcccaactcg atcgcgacca gtgtgcctac tgcaaagaaa aggggcactg ggctaaagat tgtcccaaga aaccacgagg acctcgggga ccaagacccc agacctccct cctgacccta gatgactagg gaggtcaggg tcaggagccc ccccctgaac ccaggataac cctcaaagtc ggggggcaac ccgtcacctt cctggtagat actggggccc aacactccgt gctgacccaa aatcctggac ccctaagtga taagtctgcc tgggtccaag gggctactgg aggaaagcgg tatcgctgga ccacggatcg caaagtacat ctagctaccg gtaaggtcac ccactctttc ctccatgtac cagactgtcc ctatcctctg ttaggaagag atttgctgac taaactaaaa gcccaaatcc actttgaggg atcaggagcc caggttatgg gaccaatggg gcagcccctg caagtgttga ccctaaatat agaagatgag tatcggctac atgagacctc aaaagagcca gatgtttctc tagggtccac atggctgtct gattttcctc aggcctgggc ggaaaccggg ggcatgggac tggcagttcg ccaagctcct ctgatcatac ctctgaaagc aacctctacc cccgtgtcca taaaacaata ccccatgtca caagaagcca gactggggat caagccccac atacagagac tgttggacca gggaatactg gtaccctgcc agtccccctg gaacacgccc ctgctacccg ttaagaaacc agggactaat gattataggc ctgtccagga tctgagagaa gtcaacaagc gggtggaaga catccacccc accgtgccca acccttacaa cctcttgagc gggctcccac cgtcccacca gtggtacact gtgcttgatt taaaggatgc ctttttctgc ctgagactcc accccaccag tcagcctctc ttcgcctttg agtggagaga tccagagatg ggaatctcag gacaattgac ctggaccaga ctcccacagg gtttcaaaaa cagtcccacc ctgtttgatg aggcactgca cagagaccta gcagacttcc ggatccagca cccagacttg atcctgctac agtacgtgga tgacttactg ctggccgcca cttctgagct agactgccaa caaggtactc gggccctgtt acaaacccta gggaacctcg ggtatcgggc ctcggccaag aaagcccaaa tttgccagaa acaggtcaag tatctggggt atcttctaaa agagggtcag agatggctga ctgaggccag aaaagagact gtgatggggc agcctactcc gaagacccct cgacaactaa gggagttcct agggacggca ggcttctgtc gcctctggat ccctgggttt gcagaaatgg cagccccctt gtaccctctc accaaaacgg ggactctgtt taattggggc ccagaccaac aaaaggccta tcaagaaatc aagcaagctc ttctaactgc cccagccctg gggttgccag atttgactaa gccctttgaa ctctttgtcg acgagaagca gggctacgcc aaaggtgtcc taacgcaaaa actgggacct tggcgtcggc cggtggccta cctgtccaaa aagctagacc cagtagcagc tgggtggccc ccttgcctac ggatggtagc agccattgcc gtactgacaa aggatgcagg caagctaacc atgggacagc cactagtcat tctggccccc catgcagtag aggcactagt caaacaaccc cccgaccgct ggctttccaa cgcccggatg actcactatc aggccttgct tttggacacg gaccgggtcc agttcggacc ggtggtagcc ctgaacccgg ctacgctgct cccactgcct gaggaagggc tgcaacacaa ctgccttgat atcctggccg aagcccacgg aacccgaccc gacctaacgg accagccgct cccagacgcc gaccacacct ggtacacgga tggaagcagt ctcttacaag agggacagcg taaggcggga gctgcggtga ccaccgagac cgaggtaatc tgggctaaag ccctgccagc cgggacatcc gctcagcggg ctgaactgat agcactcacc caggccctaa agatggcaga aggtaagaag ctaaatgttt atactgatag ccgttatgct tttgctactg cccatatcca tggagaaata tacagaaggc gtgggttgct cacatcagaa ggcaaagaga tcaaaaataa agacgagatc ttggccctac taaaagccct ctttctgccc aaaagactta gcataatcca ttgtccagga catcaaaagg gacacagcgc cgaggctaga ggcaaccgga tggctgacca agcggcccga aaggcagcca tcacagagac tccagacacc tctaccctcc tcatagaaaa ttcatcaccc tacacctcag aacattttca ttacacagtg actgatataa aggacctaac caagttgggg gccatttatg ataaaacaaa gaagtattgg gtctaccaag gaaaacctgt gatgcctgac cagtttactt ttgaattatt agactttctt catcagctga ctcacctcag cttctcaaaa atgaaggctc tcctagagag aagccacagt ccctactaca tgctgaaccg ggatcgaaca ctcaaaaata tcactgagac ctgcaaagct tgtgcacaag tcaacgccag caagtctgcc gttaaacagg gaactagggt ccgcgggcat cggcccggca ctcattggga gatcgatttc accgagataa agcccggatt gtatggctat aaatatcttc tagtttttat agataccttt tctggctgga tagaagcctt cccaaccaag aaagaaaccg ccaaggtcgt aaccaagaag ctactagagg agatcttccc caggttcggc atgcctcagg tattgggaac tgacaatggg cctgccttcg tctccaaggt gagtcagaca gtggccgatc tgttggggat tgattggaaa ttacattgtg catacagacc ccaaagctca ggccaggtag aaagaatgaa tagaaccatc aaggagactt taactaaatt aacgcttgca actggctcta gagactgggt gctcctactc cccttagccc tgtaccgagc ccgcaacacg ccgggccccc atggcctcac cccatatgag atcttatatg gggcaccccc gccccttgta aacttccctg accctgacat gacaagagtt actaacagcc cctctctcca agctcactta caggctctct acttagtcca gcacgaagtc tggagacctc tggcggcagc ctaccaagaa caactggacc gaccggtggt acctcaccct taccgagtcg gcgacacagt gtgggtccgc cgacaccaga ctaagaacct agaacctcgc tggaaaggac cttacacagt cctgctgacc acccccaccg ccctcaaagt agacggcatc gcagcttgga tacacgccgc ccacgtgaag gctgccgacc ccgggggtgg accatcctct agactgacat ggcgcgttca acgctctcaa aaccccctca agataagatt aacccgtgga agcccttaat agtcatggga gtcctgttag gagtagggat ggcagagagc ccccatcagg tctttaatgt aacctggaga gtcaccaacc tgatgactgg gcgtaccgcc aatgccacct ccctcctggg aactgtacaa gatgccttcc caaaattata ttttgatcta tgtgatctgg tcggagagga gtgggaccct tcagaccagg aaccgtatgt cgggtatggc tgcaagtacc ccgcagggag acagcggacc cggacttttg acttttacgt gtgccctggg cataccgtaa agtcggggtg tgggggacca ggagagggct actgtggtaa atgggggtgt gaaaccaccg gacaggctta ctggaagccc acatcatcgt gggacctaat ctcccttaag cgcggtaaca ccccctggga cacgggatgc tctaaagttg cctgtggccc ctgctacgac ctctccaaag tatccaattc cttccaaggg gctactcgag ggggcagatg caaccctcta gtcctagaat tcactgatgc aggaaaaaag gctaactggg acgggcccaa atcgtgggga ctgagactgt accggacagg aacagatcct attaccatgt tctccctgac ccggcaggtc cttaatgtgg gaccccgagt ccccataggg cccaacccag tattacccga ccaaagactc ccttcctcac caatagagat tgtaccggct ccacagccac ctagccccct caataccagt tacccccctt ccactaccag tacaccctca acctccccta caagtccaag tgtcccacag ccacccccag gaactggaga tagactacta gctctagtca aaggagccta tcaggcgctt aacctcacca atcccgacaa gacccaagaa tgttggctgt gcttagtgtc gggacctcct tattacgaag gagtagcggt cgtgggcact tataccaatc attccaccgc tccggccaac tgtacggcca cttcccaaca taagcttacc ctatctgaag tgacaggaca gggcctatgc atgggggcag tacctaaaac tcaccaggcc ttatgtaaca ccacccaaag cgccggctca ggatcctact accttgcagc acccgccgga acaatgtggg cttgcagcac tggattgact ccctgcttgt ccaccacggt gctcaatcta accacagatt attgtgtatt agttgaactc tggcccagag taatttacca ctcccccgat tatatgtatg gtcagcttga acagcgtacc aaatataaaa gagagccagt atcattgacc ctggcccttc tactaggagg attaaccatg ggagggattg cagctggaat agggacgggg accactgcct taattaaaac ccagcagttt gagcagcttc atgccgctat ccagacagac ctcaacgaag tcgaaaagtc aattaccaac ctagaaaagt cactgacctc gttgtctgaa gtagtcctac agaaccgcag aggcctagat ttgctattcc taaaggaggg aggtctctgc gcagccctaa aagaagaatg ttgtttttat gcagaccaca cggggctagt gagagacagc atggccaaat taagagaaag gcttaatcag agacaaaaac tatttgagac aggccaagga tggttcgaag ggctgtttaa tagatccccc tggtttacca ccttaatctc caccatcatg ggacctctaa tagtactctt actgatctta ctctttggac cttgcattct caatcgattg gtccaatttg ttaaagacag gatctcagtg gtccaggctc tggttttgac tcagcaatat caccagctaa aacccataga gtacgagcca tgaacgcgtt actggccgaa gccgcttgga ataaggccgg tgtgcgtttg tctatatgtt attttccacc atattgccgt cttttggcaa tgtgagggcc cggaaacctg gccctgtctt cttgacgagc attcctaggg gtctttcccc tctcgccaaa ggaatgcaag gtctgttgaa tgtcgtgaag gaagcagttc ctctggaagc ttcttgaaga caaacaacgt ctgtagcgac cctttgcagg cagcggaacc ccccacctgg cgacaggtgc ctctgcggcc aaaagccacg tgtataagat acacctgcaa aggcggcaca accccagtgc cacgttgtga gttggatagt tgtggaaaga gtcaaatggc tctcctcaag cgtattcaac aaggggctga aggatgccca gaaggtaccc cattgtatgg gatctgatct ggggcctcgg tgcacatgct ttacatgtgt ttagtcgagg ttaaaaaaac gtctaggccc cccgaaccac ggggacgtgg ttttcctttg aaaaacacga ttataaatgg tgaccggcgg catggcctcc aagtgggatc aaaagggcat ggatatcgct tacgaggagg ccctgctggg ctacaaggag ggcggcgtgc ctatcggcgg ctgtctgatc aacaacaagg acggcagtgt gctgggcagg ggccacaaca tgaggttcca gaagggctcc gccaccctgc acggcgagat ctccaccctg gagaactgtg gcaggctgga gggcaaggtg tacaaggaca ccaccctgta caccaccctg tccccttgtg acatgtgtac cggcgctatc atcatgtacg gcatccctag gtgtgtgatc ggcgagaacg tgaacttcaa gtccaagggc gagaagtacc tgcaaaccag gggccacgag gtggtggttg ttgacgatga gaggtgtaag aagctgatga agcagttcat cgacgagagg cctcaggact ggttcgagga tatcggcgag taagcggccg cagataaaat aaaagatttt atttagtctc cagaaaaagg ggggaatgaa agaccccacc tgtaggtttg gcaagctagc ttaagtaacg ccattttgca aggcatggaa aaatacataa ctgagaatag agaagttcag atcaaggtca ggaacagatg gaacagctga atatgggcca aacaggatat ctgtggtaag cagttcctgc cccggctcag ggccaagaac agatggaaca gctgaatatg ggccaaacag gatatctgtg gtaagcagtt cctgccccgg ctcagggcca agaacagatg gtccccagat gcggtccagc cctcagcagt ttctagagaa ccatcagatg tttccagggt gccccaagga cctgaaatga ccctgtgcct tatttgaact aaccaatcag ttcgcttctc gcttctgttc gcgcgcttct gctccccgag ctcaataaaa gagcccacaa cccctcactc ggggcgccag tcctccgatt gactgagtcg cccgggtacc cgtgtatcca ataaaccctc ttgcagttgc atccgacttg tggtctcgct gttccttggg agggtctcct ctgagtgatt gactacccgt cagcgggggt ctttcattac atgtgagcaa aaggccagca aaaggccagg aaccgtaaaa aggccgcgtt gctggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag tcagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgctgtagg tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac gacttatcgc cactggcagc agccactggt aacaggatta gcagagcgag gtatgtaggc ggtgctacag agttcttgaa gtggtggcct aactacggct acactagaag gacagtattt ggtatctgcg ctctgctgaa gccagttacc ttcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga agatcctttg atcttttcta cggggtctga cgctcagtgg aacgaaaact cacgttaagg gattttggtc atgagattat caaaaaggat cttcacctag atccttttaa attaaaaatg aagttttaaa tcaatctaaa gtatatatga gtaaacttgg tctgacagtt accaatgctt aatcagtgag gcacctatct cagcgatctg tctatttcgt tcatccatag ttgcctgact ccccgtcgtg tagataacta cgatacggga gggcttacca tctggcccca gtgctgcaat gataccgcga gacccacgct caccggctcc agatttatca gcaataaacc agccagccgg aagggccgag cgcagaagtg gtcctgcaac tttatccgcc tccatccagt ctattaattg ttgccgggaa gctagagtaa gtagttcgcc agttaatagt ttgcgcaacg ttgttgccat tgctgcaggc atcgtggtgt cacgctcgtc gtttggtatg gcttcattca gctccggttc ccaacgatca aggcgagtta catgatcccc catgttgtgc aaaaaagcgg ttagctcctt cggtcctccg atcgttgtca gaagtaagtt ggccgcagtg ttatcactca tggttatggc agcactgcat aattctctta ctgtcatgcc atccgtaaga tgcttttctg tgactggtga gtactcaacc aagtcattct gagaatagtg tatgcggcga ccgagttgct cttgcccggc gtcaacacgg gataataccg cgccacatag cagaacttta aaagtgctca tcattggaaa acgttcttcg gggcgaaaac tctcaaggat cttaccgctg ttgagatcca gttcgatgta acccactcgt gcacccaact gatcttcagc atcttttact ttcaccagcg tttctgggtg agcaaaaaca ggaaggcaaa atgccgcaaa aaagggaata agggcgacac ggaaatgttg aatactcata ctcttccttt ttcaatatta ttgaagcatt tatcagggtt attgtctcat gagcggatac atatttgaat gtatttagaa aaataaacaa ataggggttc cgcgcacatt tccccgaaaa gtgccacctg acgtctaaga aaccattatt atcatgacat taacctataa aaataggcgt atcacgaggc cctttcgtct tcaagaattc cat

Disclosed herein are assays for detection of target molecules, such as target nucleic acids comprising viral RNA or DNA, using a plurality of nucleic acid amplification techniques including, for example: NAAT (J. D. Fox, J. Clin. Virol. 40 Suppl. 1 S15-S23, 2007), PCR, RT-PCR, qPCR and RT-qPCR with “touchdown” modifications to improve sensitivity to single copy/assay; RNA transcription based assays (e.g. analogous to the HIV-1 Aptiva assay, see http:(//)www.fda.gov/BiologicsBloodVaccines/BloodBloodProducts/ApprovedProducts/LicensedProductsBLAs/BloodDonor Screening/InfectiousDisease/ucm1 49922.htm); the “branched DNA” system (see, e.g., Anastassopoulou et al., Journal of Virological Methods, 91:67-74, 2001); and further variations in NAAT known to those of skill in the art. Also disclosed are methods using NAAT on nucleic acid samples extracted from histologically fixed samples.

The assays provided by the disclosure may be used in many embodiments to detect sequence-specific nucleic acids. Disclosed herein are different embodiments of assays using amplification (e.g., PCR) and enzymatic degradation of RNA/DNA heteroduplexes.

Generally, the disclosure provides a method of identifying MLV-related viral polynucleotides in a subject or sample. The disclosure utilizes a combination of primers and probes having identity to conserved regions of MLV-related viruses. The primers are used to amplify target polynucleotides in the sample and probes are then used to visualize or detect the amplified products. Typically the probe is detectably labeled for detection (e.g., fluorescently labeled, luminescently labeled, enzyme conjugated, radionucleotide labeled and the like). One advantage of the disclosure is that the primer pairs can be used to amplify MLV-related polynucleotides in a sample such as MLV, XMRV or MLV and XMRV polynucleotides. This is advantageous for the detection of XMRV and naturally occurring variants thereof as well as for detecting MLV and naturally occurring variants thereof (including recombinantly engineered MLV vectors).

For example, a combination of primers and probes identified herein can be used to identify or detect XMRV in a sample, tissue or subject by using primer pairs having homology to MLV (e.g., primer pairs that share at least 95% sequence identity between and XMRV viral sequence and an MLV viral sequence) and a probe sequence that is specific for XMRV (e.g., the probe only hybridizes to an amplified product under highly stringent conditions). Primers that share such homology between XMRV and MLV are identified in FIG. 5 and Table 2.

One utility of this general method is to screen blood and tissue supplies for infection. XMRV has been suggested to be associated with prostate cancer and chronic fatigue syndrome. In another utility, a subject may be screened prior to undergoing treatment with a recombinant retroviral vector. By identifying subject that may have circulating viral polynucleotides in the tissue a risk of recombination between the inherent viral polynucleotide and the therapeutic viral polynucleotide may be managed.

In another general example, a combination of primers and probes identified herein can be used to identify or detect MLV or MLV-related polynucleotides in a sample, tissue or subject by using primer pairs having homology to MLV (e.g., primer pairs that share at least 95% sequence identity between and XMRV viral sequence and an MLV viral sequence) and a probe sequence that is specific for MLV (e.g., the probe only hybridizes to an amplified product under highly stringent conditions).

In another embodiment of the general methods described herein, the methods provide useful diagnostics for monitoring patients after delivery of a replication competent MLV-related viral vector. The method can be used to monitor a subject following delivery of the vector on a routine basis (e.g., weekly, monthly, yearly) for as long as a treating physician deems necessary.

As used herein “MLV-related virus” refers to a retrovirus comprising the general structure of an MLV virus (e.g., LTR-gag-pol-env-LTR) and having at least 60% identity to any of the following sequences set forth in the identified accession numbers (which are incorporated herein by reference in their entirety):

Xenotropic murine leukemia virus isolate LAPC4, complete genome (8,657 bp linear DNA, JF908816.1 GI:336462519); Xenotropic murine leukemia virus isolate VCaP, complete genome (8,657 bp linear DNA, JF908815.1 GI:336462515); Murine leukemia virus N417, complete genome (8,189 bp linear RNA, HQ246218.1 GI:313762331); Moloney murine leukemia virus neuropathogenic variant ts1-92b, complete genome (8,332 bp linear DNA, AF462057.1 GI:18448741); DG-75 Murine leukemia virus, complete genome (8,207 bp linear RNA, AF221065.1 GI:11078528); Rauscher murine leukemia virus, complete genome (8,282 bp linear DNA, NC_(—)001819.1 GI:9629514); Murine leukemia virus SL3-3, complete genome (8,377 bp linear RNA, AF169256.1 GI:5881088); Murine leukemia virus strain SRS 19-6 complete genome (8,256 bp linear DNA, AF019230.1 GI:4071074); Mus dunni endogenous virus complete genome (8,655 bp linear DNA, AF053745.1 GI:3309122); Moloney murine leukemia virus, complete genome (8,332 bp linear RNA, AF033811.1 GI:2801468); Murine type C retrovirus, complete genome (8,135 bp linear DNA, NC_(—)001702.1 GI:9628654); Rauscher murine leukemia virus, complete genome (8,282 bp linear DNA, U94692.1 GI:2228757); Murine leukemia virus isolate NeRV, complete genome (8,273 bp linear RNA, DQ366149.1 GI:86651892); Murine leukemia virus serotype HEMV provirus, complete genome (8,546 bp linear DNA, AY818896.1 GI:55979252); Murine leukemia virus strain BMSeco, complete genome (8,281 bp linear DNA, AY252102.1 GI:30908470); Murine leukemia virus MCF1233, complete genome (8,196 bp linear DNA, U13766.1 GI:535516); MuLV (strain RadLV/VL3(T+L+)) RNA, complete genome (8,394 bp linear RNA, K03363.1 GI:332032); Mink cell focus-forming 247 MuLV env gene, 3′ end and LTR (1,164 bp linear RNA, J02249.1 GI:332023); Friend murine leukemia virus, complete genome (8,282 bp linear RNA, M93134.1 GI:331898); Friend murine leukemia virus, complete genome (8,323 bp linear RNA, NC_(—)001362.1 GI:9626096); Friend murine leukemia virus (F-MuLV) complete RNA genome (8,359 bp linear RNA, X02794.1 GI:61544); Gallus gallus MLV-related endogenous retrovirus, complete genome (9,133 bp linear DNA, DQ280312.2 GI:169805278); Friend murine leukemia virus genomic RNA, complete genome, clone:A8 (8,358 bp linear RNA, D88386.1 GI:2351211); PreXMRV-1 provirus, complete genome (8,197 bp linear DNA; NC_(—)007815.2 GI:339276104); Xenotropic MuLV-related virus RKO, complete genome (8,172 bp linear DNA, JF274252.1 GI:338191621); XMRV complete proviral genome, isolate S-162 (8,562 bp linear DNA, FR872816.1 GI:336087897); PreXMRV-2 complete proviral genome (8,193 bp linear DNA, FR871850.1 GI:334849718); Xenotropic MuLV-related virus 22Rv1/CWR-R1 complete proviral genome (8,185 bp linear DNA, FN692043.2 GI:334717372); Xenotropic MuLV-related virus isolate xm1v15, complete genome (8,176 bp linear RNA, HQ154630.1 GI:320091412); PreXMRV-1 complete proviral genome (8,197 bp linear DNA, FR871849.1 GI:334849715); Xenotropic MuLV-related virus VP62, complete genome (8,185 bp linear RNA, DQ399707.1 GI:88765817); Xenotropic MuLV-related virus VP42, complete genome (8,185 bp linear RNA, DQ241302.1 GI:82582299); Xenotropic MuLV-related virus VP35, complete genome (8,185 bp linear RNA, DQ241301.1 GI:82582295); Xenotropic MuLV-related virus VP62, complete genome (8,165 bp linear RNA, EF185282.1 GI:121104176); Plasmid pAMS with hybrid amphotropic/Moloney murine leukemia virus, complete sequence (11,328 bp circular DNA, AF010170.1 GI:2281586); Amphotropic murine leukemia virus strain 1313, complete genome (8,217 bp linear DNA, AF411814.1 GI:28892668); Toca511, recombinant replication competent MLV comprising a polynucleotide encoding cytosine deaminase (see, e.g., SEQ ID NO:19, 20 and 22 of PCT/US2009/058512, incorporated herein by reference).

Any number of different alignment programs can be used to identified regions of identity between any combination of the foregoing MLV-related genomes. Other genomes will be readily identified by using a BLAST algorithm or other similar algorithm to identify sequences having homology/identity to the foregoing sequences.

In some embodiments the disclosure relates to a method of detecting MLV-related viruses including XMRV in a sample comprising contacting the sample with a nucleic acid sequence that hybridizes to all or a portion of XMRV nucleic acid sequence under conditions in which a hybridization complex can occur between the detecting nucleic acid sequence and the XMRV nucleic acid sequence. In a related embodiment, the XMRV specific primers are 95% or more identical to SEQ ID Nos:1 and 2, and the probe is 95% or more identical to SEQ ID NO:3 (XMRV gag). In a further related embodiment the XMRV specific primers are 95% or more identical to SEQ ID NOs:4 and 5 and the probe is 95% or more identical to SEQ ID NO:6 (XMRV env). In yet a further embodiment, the method uses a combination of primers and probes (e.g., SEQ ID NO:1, 2, 4 and 5 and probes comprising SEQ ID NO:3 and 6).

In another embodiment, the disclosure relates to a method of detecting XMRV or other MLV related nucleic acids in a sample by using primers and probes that are not specific to XMRV but rather are shared between XMRV and other related strains of MLV. In a related embodiment the MLV/XMRV specific primers are SEQ ID NOs:7 and 8 and the probe is SEQ ID NO:9 (Pol 2 primers and probe; other primers and probes are set forth in Table 1, 2, 3, and 4 below). In a further related embodiment, the MLV/XMRV specific primers are SEQ ID NOs:10 and 11 and the probe is SEQ ID NO:12 (pol1 primer and probe). In a further related embodiment, other sequences can be identified that are common to XMRV and MLV (see the BLAST sequence comparison of two genomes of XMRV and MLV, FIG. 5, where perfect sequence homologies of 20 or more bases are underlined/highlighted). Such homologous sequences (or shorter runs of homology down to 15 bases) can be used to select primers and probes. Alternatively, primers and probes can be chosen using programs that compare sequences and suggest common primers and probes. Such programs are usually designed to look for related genes in different species, and can be used to design QPCR reagents for molecules such as MLV and XMRV with significant but incomplete homology. An example of such a program is Primaclade http:(//)www.umsl.edu/services/kellogg/primaclade/FAQ.html.

An oligonucleotide probe or a primer refers to a nucleic acid molecule of between 8 and 2000 nucleotides in length, or is specified to be about 6 and 1000 nucleotides in length. More particularly, the length of these oligonucleotides can range from about 8, 10, 15, 20, or 30 to 100 nucleotides, but will typically be about 10 to 50 (e.g., 15 to 30 nucleotides). The appropriate length for oligonucleotides in assays of the disclosure under a particular set of conditions may be empirically determined by one of skill in the art. As used herein a primer or probe consisting of at least 95% identity to a reference sequence means that the sequence comprises a sequence that is the same number of oligonucleotides in length, but may differ in nucleotides by 5% from the reference sequence. In addition, a primer or probe consisting of at least 95% identity to a reference sequence and having from 1-10 additional or deleted nucleotides at the 5′ and/or 3′ end of the oligonucleotide means that the sequence differs by 1 to up to 20 nucleotides in length from the reference sequence and which also differs 5% or less in identity. Accordingly, any primer probe disclosed herein by consist of a reference sequence (e.g., SEQ ID NO:1-21 or sequences set forth in Table 1 and 2); can consist of a sequence that is 95% of greater in identity to a reference sequence (e.g., SEQ ID NO:1-21 or sequences set forth in Table 1 and 2); or can consist of a sequence that is at least 95% identical and has an additional 1-20 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides at the 5′ and/or 3′ end of the reference sequence (e.g., SEQ ID NO:1-21 or sequence set forth in Table 1 and 2).

Oligonucleotide primers and probes can be prepared by any suitable method, including direct chemical synthesis and a number of probe systems with derivatized oligonucleotides are available to hybridize to and to detect amplified product, normally by fluorescence change on binding to the probe target. The oligonucleotide primers and probes can contain conventional nucleotides, as well as any of a variety of analogs. For example, the term “nucleotide”, as used herein, refers to a compound comprising a nucleotide base linked to the C-1′ carbon of a sugar, such as ribose, arabinose, xylose, and pyranose, and sugar analogs thereof. The term nucleotide also encompasses nucleotide analogs. The sugar may be substituted or unsubstituted. Substituted ribose sugars include, but are not limited to, those riboses in which one or more of the carbon atoms, for example the 2′-carbon atom, is substituted with one or more of the same or different Cl, F, —R, —OR, —NR₂ or halogen groups, where each R is independently H, C₁-C₆ alkyl or C₅-C₁₄ aryl. Exemplary riboses include, but are not limited to, 2′-(C₁-C₆)alkoxyribose, 2′-(C₅-C₁₄)aryloxyribose, 2′,3′-didehydroribose, 2′-deoxy-3′-haloribose, 2′-deoxy-3′-fluororibose, 2′-deoxy-3′-chlororibose, 2′-deoxy-3′-aminoribose, 2′-deoxy-3′-(C₁-C₆)alkylribose, 2′-deoxy-3′-(C₁-C₆)alkoxyribose and 2′-deoxy-3′-(C₅-C₁₄)aryloxyribose, ribose, 2′-deoxyribose, 2′,3′-dideoxyribose, 2′-haloribose, 2′-fluororibose, 2′-chlororibose, and 2′-alkylribose, e.g., 2′-O-methyl, 4′-α-anomeric nucleotides, 1′-α-anomeric nucleotides, 2′-4′- and 3′-4′-linked and other “locked” or “LNA”, bicyclic sugar modifications (see, e.g., PCT published application nos. WO 98/22489, WO 98/39352; and WO 99/14226).

Modifications at the 2′- or 3′-position of ribose include, but are not limited to, hydrogen, hydroxy, methoxy, ethoxy, allyloxy, isopropoxy, butoxy, isobutoxy, methoxyethyl, alkoxy, phenoxy, azido, amino, alkylamino, fluoro, chloro and bromo. Nucleotides include, but are not limited to, the natural D optical isomer, as well as the L optical isomer forms (see, e.g., Garbesi (1993) Nucl. Acids Res. 21:4159-65; Fujimori (1990) J. Amer. Chem. Soc. 112:7435; Urata, (1993) Nucleic Acids Symposium Ser. No. 29:69-70). When the nucleotide base is purine, e.g. A or G, the ribose sugar is attached to the N₉-position of the nucleotide base. When the nucleotide base is pyrimidine, e.g. C, T or U, the pentose sugar is attached to the N₁-position of the nucleotide base, except for pseudouridines, in which the pentose sugar is attached to the C₅ position of the uracil nucleotide base (see, e.g., Kornberg and Baker, (1992) DNA Replication, 2nd Ed., Freeman, San Francisco, Calif.). The 3′ end of the probe can be functionalized with a capture or detectable label to assist in detection of a target polynucleotide or of a polymorphism.

Any of the oligonucleotides or nucleic acids of the disclosure can be labeled by incorporating a detectable label measurable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. For example, such labels can comprise radioactive substances (e.g., ³²P, ³⁵S, ³H, ¹²⁵I) fluorescent dyes (e.g., 5-bromodesoxyuridin, fluorescein, acetylaminofluorene, digoxigenin), molecular quenchers (e.g. blackhole, molecular beacons), biotin, nanoparticles, and others know to those skilled in the art. Such oligonucleotides are typically labeled at their 3′ and/or 5′ ends.

A probe refers to a molecule which can detectably distinguish changes in gene expression or can distinguish between target molecules differing in structure. Detection can be accomplished in a variety of different ways depending on the type of probe used and the type of target molecule. Thus, for example, detection may be based on discrimination of activity levels of the target molecule, but typically is based on detection of specific binding. Examples of such specific binding include nucleic acid probe hybridization. Thus, for example, probes can include nucleic acid hybridization probes (including primers useful for polynucleotide amplification and/or detection). Thus, in one embodiment, the detection of the presence or absence of the at least one target polynucleotide involves contacting a biological sample with a probe or primer pair. Typically an oligonucleotide probe or primer pair, where the probe/primers hybridizes with a form of a target polynucleotide in the biological sample containing a complementary sequence, undergoes hybridization using hybridization selective conditions. Such an oligonucleotide probe can include one or more nucleic acid analogs, labels or other substituents or moieties so long as the base-pairing function is retained.

The disclosure provides methods and systems for identifying and quantifying the amount of a given nucleic acid sequence in a given sample, usually down to a single copy per sample. Furthermore, the methods and systems of the disclosure provide sequence specific detection useful for differentiating/identifying related genomic sequences and provide a detectable signal when the correct target sequence is present. The disclosure provides various embodiments of the invention.

Methods known in the art can be used to quantitatively measure the amount of a nucleic acid present in a sample. Examples of such methods include quantitative polymerase chain reaction (qPCR), and other NAAT technologies as described above.

In one embodiment, a method for detecting a specific viral polynucleotide is provided by the disclosure. Such a method can include the use of primers, probes, enzymes, and other reagents for the preparation, detection, and quantitation of a viral polynucleotide (e.g., by PCR, by Northern blot and the like). The primers listed in SEQ ID NOs: 1-12 are particularly suited for use in profiling using RT-PCR based on a viral polynucleotide. Other primers (sense and antisense) and probes are provided in Table 2. One of skill in the art can readily identity in Table 2, the combinations of primer/probes useful for detection of an MLV, MLV-related or XMRV viral sequence. Although the disclosure provides particular primers and probes, those of skill in the art will readily recognize that additional probes and primers can be generated based upon the polynucleotide sequences provided by the disclosure (see, also, for example, FIG. 5). Referring to the primers and probes exemplified herein, a series of primers were designed to amplify portions of a murine retroviral (MLV) genome. The primer/probe sets listed in SEQ ID NOs: 1-12 were designed, selected, and tested accordingly (see Examples). Though a number of detection schemes for detecting amplicons are contemplated, as will be discussed in more detail below, one method for detection of polynucleotide amplicons is fluorescence spectroscopy, and therefore labels suited to fluorescence spectroscopy are desirable for detecting polynucleotide. In a related form of detection the amplicon polynucleotide is detected without a hybridization probe but directly with a fluorophore that binds DNA and fluoresces at a wavelength different from that of the free reagent. An example of such a fluorescent label is SYBR Green, though numerous related fluorescent molecules are known including, without limitation, DAPI, Cy3, Cy3.5, Cy5, CyS.5, Cy7, umbelliferone, fluorescein, fluorescein isothiocyanate (FITC), rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin.

In one embodiment of the disclosure, an oligonucleotide primer pair is used to amplify a polynucleotide corresponding to the pol gene of a murine retrovirus. Primers comprising SEQ ID NOs:7 and 8 (forward and reverse primers, respectively) are used to amplify the region of the pol gene. The amplified region can then be detected using a probe (SEQ ID NO:9), which specifically hybridizes to the amplified polynucleotide. The probe can be labeled with any number of detectable labels as described herein.

The foregoing primers (SEQ ID NOs:7, 8 and 10, 11) with the appropriate probes (SEQ ID NOs:9 and 12, respectively) can be used to detect the presence of, for example, Murine Leukemia Virus (MLV) and Xenotropic Murine Retrovirus (XMRV). As described elsewhere herein identifying the presence of MLV and/or XMRV is useful for the determination of a therapeutic gene delivery and cancer treatment regimen.

In another embodiment of the disclosure, an oligonucleotide primer pair is used to amplify a polynucleotide corresponding to the gag gene of a XMRV. Primers comprising SEQ ID NOs:1 and 2 (forward and reverse primers, respectively) are used to amplify the region of the gag gene of XMRV. The amplified region can then be detected using a probe (SEQ ID NO:3) which specifically hybridizes to the amplified polynucleotide. The probe can be labeled with any number of detectable labels as described herein. This combination of primers and probes is useful for specifically identifying the presence of an XMRV infection or contamination.

In another embodiment of the disclosure, an oligonucleotide primer pair is used to amplify a polynucleotide corresponding to the LTR of an MLV vector. Primers comprising SEQ ID NOs:16 and 17 (forward and reverse primers, respectively) are used to amplify the region of the LTR of an MLV vector (e.g., Toca511). The amplified region can then be detected using a probe (SEQ ID NO:18) which specifically hybridizes to the amplified polynucleotide. The probe can be labeled with any number of detectable labels as described herein. This combination of primers and probes is useful for specifically identifying the presence of a retroviral vector during gene delivery monitoring.

In another embodiment of the disclosure, an oligonucleotide primer pair is used to amplify a polynucleotide corresponding to a polynucleotide encoding a cytosine deaminase. Primers comprising SEQ ID NOs:19 and 20 (forward and reverse primers, respectively) are used to amplify the region of the a cytosine deaminase delivered using an MLV vector (e.g., Toca511). The amplified region can then be detected using a probe (SEQ ID NO:21) which specifically hybridizes to the amplified polynucleotide. The probe can be labeled with any number of detectable labels as described herein. This combination of primers and probes is useful for specifically identifying the presence of a retroviral vector during gene delivery monitoring.

The primers (SEQ ID NOs: 1 and 2) and probe (SEQ ID NO:3) can be used to detect the presence of XMRV. As described elsewhere herein identifying the presence of XMRV is useful for the determination of a therapeutic gene delivery, cancer treatment regimen and blood supply screening.

In another embodiment of the disclosure, an oligonucleotide primer pair is used to amplify a polynucleotide corresponding to the env gene of a XMRV. Primers comprising SEQ ID NOs:4 and 5 (forward and reverse primers, respectively) are used to amplify the region of the env gene of XMRV. The amplified region can then be detected using a probe (SEQ ID NO:6) which specifically hybridizes to the amplified polynucleotide. The probe can be labeled with any number of detectable labels as described herein. This combination of primers and probes is useful for specifically identifying the presence of an XMRV infection or contamination.

The foregoing primers (SEQ ID NOs:4 and 5) and probe (SEQ ID NO:6) can be used to detect the presence of XMRV. As described elsewhere herein identifying the presence of XMRV is useful for the determination of a therapeutic gene delivery, cancer treatment regimen and screening the blood supply.

Any of the oligonucleotide primers and probes of the disclosure can be immobilized on a solid support. Solid supports are known to those skilled in the art and include the walls of wells of a reaction tray, test tubes, polystyrene beads, magnetic beads, nitrocellulose strips, membranes, microparticles such as latex particles, glass and the like. The solid support is not critical and can be selected by one skilled in the art. Thus, latex particles, microparticles, magnetic or non-magnetic beads, membranes, plastic tubes, walls of microtiter wells, glass or silicon chips and the like are all suitable examples. Suitable methods for immobilizing oligonucleotides on a solid phase include ionic, hydrophobic, covalent interactions and the like. The solid support can be chosen for its intrinsic ability to attract and immobilize the capture reagent. The oligonucleotide probes or primers of the disclosure can be attached to or immobilized on a solid support individually or in groups of about 2-10,000 distinct oligonucleotides of the disclosure to a single solid support.

A substrate comprising a plurality of oligonucleotide primers or probes of the disclosure may be used either for detecting or amplifying targeted sequences. The oligonucleotide probes and primers of the disclosure can be attached in contiguous regions or at random locations on the solid support. Alternatively the oligonucleotides of the disclosure may be attached in an ordered array wherein each oligonucleotide is attached to a distinct region of the solid support which does not overlap with the attachment site of any other oligonucleotide. Typically, such oligonucleotide arrays are “addressable” such that distinct locations are recorded and can be accessed as part of an assay procedure. The knowledge of the location of oligonucleotides on an array make “addressable” arrays useful in hybridization assays. For example, the oligonucleotide probes can be used in an oligonucleotide chip such as those marketed by Affymetrix and described in U.S. Pat. No. 5,143,854; PCT publications WO 90/15070 and 92/10092, the disclosures of which are incorporated herein by reference. These arrays can be produced using mechanical synthesis methods or light directed synthesis methods which incorporate a combination of photolithographic methods and solid phase oligonucleotide synthesis.

The immobilization of arrays of oligonucleotides on solid supports has been rendered possible by the development of a technology generally referred to as “Very Large Scale Immobilized Polymer Synthesis” in which probes are immobilized in a high density array on a solid surface of a chip (see, e.g., U.S. Pat. Nos. 5,143,854; and 5,412,087 and in PCT Publications WO 90/15070, WO 92/10092 and WO 95/11995, each of which are incorporated herein by reference), which describe methods for forming oligonucleotide arrays through techniques such as light-directed synthesis techniques.

In another embodiment, an array of oligonucleotides complementary to subsequences of the target gene (for example yeast cytosine deaminase (CD) or a version of CD optimized for expression in human cells) is used to determine the identity of the target, measure its amount and the like.

Hybridization techniques can also be used to identify the viral polynucleotides in a subject or sample and thereby determine or predict cross reactivity, chances of recombination or a treatment regimen using a gene delivery vector comprising a recombinant MLV vector. The hybridization reactions may be carried out in a solid support (e.g., membrane or chip) format, in which, for example, a probe (e.g., SEQ ID NO:3, 6 and/or 9) are immobilized on nitrocellulose or nylon membranes and probed with amplified preparations of nucleic acids obtained, for example, from PCR using primers comprising SEQ ID NO:1, 2, 4, 5, 7, 8, 10, 11, 13 and/or 14 of the disclosure. Any of the known hybridization formats may be used, including Southern blots, slot blots, “reverse” dot blots, solution hybridization, solid support based sandwich hybridization, bead-based, silicon chip-based and microtiter well-based hybridization formats.

Hybridization of an oligonucleotide probe to a target polynucleotide may be performed with both entities in solution, or such hybridization may be performed when either the oligonucleotide or the target polynucleotide is covalently or noncovalently affixed to a solid support. Attachment to a solid support may be mediated, for example, by antibody-antigen interactions, poly-L-Lysine, streptavidin or avidin-biotin, salt bridges, hydrophobic interactions, chemical linkages, UV cross-linking baking, etc. Oligonucleotides may be synthesized directly on the solid support or attached to the solid support subsequent to synthesis. The solid support may be treated, coated or derivatized to facilitate the immobilization of the specific oligonucleotide.

Hybridization assays based on oligonucleotide arrays rely on the differences in hybridization stability of short oligonucleotides to perfectly matched and mismatched target variants. Each DNA chip can contain thousands to millions of individual synthetic DNA probes arranged in a grid-like pattern and miniaturized to the size of a dime or smaller. Such a chip may comprise oligonucleotides representative of both a wild-type and variant sequences.

Oligonucleotides of the disclosure can be designed to specifically hybridize to a target region of a polynucleotide. As used herein, specific hybridization means the oligonucleotide forms an anti-parallel double-stranded structure with the target region under certain hybridizing conditions, while failing to form such a structure when incubated with a different target polynucleotide or another region in the polynucleotide or with a polynucleotide lacking the desired locus under the same hybridizing conditions. Typically, the oligonucleotide specifically hybridizes to the target region under conventional high stringency conditions.

A nucleic acid molecule such as an oligonucleotide or polynucleotide is said to be a “perfect” or “complete” complement of another nucleic acid molecule if every nucleotide of one of the molecules is complementary to the nucleotide at the corresponding position of the other molecule. A nucleic acid molecule is “substantially complementary” to another molecule if it hybridizes to that molecule with sufficient stability to remain in a duplex form under conventional low-stringency conditions. Conventional hybridization conditions are described, for example, in Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd ed., Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989), and in Haymes et al., Nucleic Acid Hybridization, A Practical Approach, IRL Press, Washington, D.C. (1985). While perfectly complementary oligonucleotides are used in most assays for detecting target polynucleotides or polymorphisms, departures from complete complementarity are contemplated where such departures do not prevent the molecule from specifically hybridizing to the target region. For example, an oligonucleotide primer may have a non-complementary fragment at its 5′ or 3′ end, with the remainder of the primer being complementary to the target region. Those of skill in the art are familiar with parameters that affect hybridization; such as temperature, probe or primer length and composition, buffer composition and salt concentration and can readily adjust these parameters to achieve specific hybridization of a nucleic acid to a target sequence.

A variety of hybridization conditions may be used in the disclosure, including high, moderate and low stringency conditions; see for example Maniatis et al., Molecular Cloning: A Laboratory Manual, 2d Edition, 1989, and Short Protocols in Molecular Biology, ed. Ausubel, et al., hereby incorporated by reference. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, stringent conditions are selected to be about 5-10° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength and pH. The T_(m) is the temperature (under defined ionic strength, pH and nucleic acid concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at T_(m), 50% of the probes are occupied at equilibrium). Stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of helix destabilizing agents such as formamide. The hybridization conditions may also vary when a non-ionic backbone, i.e., PNA is used, as is known in the art. In addition, cross-linking agents may be added after target binding to cross-link, i.e., covalently attach, the two strands of the hybridization complex.

Methods and compositions of the disclosure are useful for diagnosing or determining the presence of contamination or infection in a sample or subject, respectively. Such tests can be performed using DNA or RNA samples collected from blood, cells, biopsies, tissue scrapings, tissue culture, or other cellular materials. As will be appreciated by those in the art, target polynucleotides can be obtained from samples including, but not limited to, bodily fluids (e.g., blood, urine, serum, lymph, saliva, anal and vaginal secretions, perspiration and semen) of virtually any organism, with mammalian samples common to the methods of the disclosure and human samples being typical. The sample may comprise individual cells, including primary cells (including bacteria) and cell lines including, but not limited to, tumor cells of all types (particularly melanoma, myeloid leukemia, carcinomas of the lung, breast, ovaries, colon, kidney, prostate, pancreas and testes); cardiomyocytes; endothelial cells; epithelial cells; lymphocytes (T-cell and B cell); mast cells; eosinophils; vascular intimal cells; hepatocytes; leukocytes including mononuclear leukocytes; stem cells such as haemopoetic, neural, skin, lung, kidney, liver and myocyte stem cells; osteoclasts; chondrocytes and other connective tissue cells; keratinocytes; melanocytes; liver cells; kidney cells; and adipocytes. Suitable cells also include known research cells, including, but not limited to, Jurkat T cells, NIH3T3 cells, CHO, Cos, 923, HeLa, SiHa, WI-38, Weri-1, MG-63, and the like (see the ATCC cell line catalog, hereby expressly incorporated by reference).

Other methods to amplify and identify viral infection or contamination by MLV or XMRV will be recognized in the art and can be utilized in combination with the primers and probes identified herein. For example, one of skill in the art will recognize that Branched DNA, Hybrid Capture Assays, PCR (including RT, nested, multiplex, Real Time), Nucleic acid sequence-based amplification, transcription mediated amplification, strand displacement amplification, Ligase Chain Reaction, Cleavase-invader technology and cycling probe technology can be used with the oligonucleotides of the disclosure.

A target polynucleotide (e.g., a virus polynucleotide or gene) may be amplified using any oligonucleotide-directed amplification method including, but not limited to, polymerase chain reaction (PCR) (U.S. Pat. No. 4,965,188), ligase chain reaction (LCR) (Barany et al., Proc. Natl. Acad. Sci. USA 88:189-93 (1991); WO 90/01069), and oligonucleotide ligation assay (OLA) (Landegren et al., Science 241:1077-80 (1988)). Other known nucleic acid amplification procedures may be used to amplify the target region (s) including transcription-based amplification systems (U.S. Pat. No. 5,130,238; European Patent No. EP 329,822; U.S. Pat. No. 5,169,766; WO 89/06700) and isothermal methods (Walker et al., Proc. Natl. Acad. Sci. USA 89:392-6 (1992)).

Ligase Chain Reaction (LCR) techniques can be used and are particularly useful for detection of single or multiple (e.g., 1, 2, 3, 4, or 5) nucleotide differences between similar polynucleotides. LCR occurs only when the oligonucleotides are correctly base-paired. The Ligase Chain Reaction (LCR), which utilizes the thermostable Taq ligase for ligation amplification, is useful for interrogating loci of a gene. LCR differs from PCR because it amplifies the probe molecule rather than producing amplicon through polymerization of nucleotides. Two probes are used per each DNA strand and are ligated together to form a single probe. LCR uses both a DNA polymerase enzyme and a DNA ligase enzyme to drive the reaction. Like PCR, LCR requires a thermal cycler to drive the reaction and each cycle results in a doubling of the target nucleic acid molecule. LCR can have greater specificity than PCR. The elevated reaction temperatures permit the ligation reaction to be conducted with high stringency. Where a mismatch occurs, ligation cannot be accomplished. For example, a probe based upon a target polynucleotide is synthesized in two fragments and annealed to the template with possible difference at the boundary of the two primer fragments. A ligase ligates the two primers if they match exactly to the template sequence.

In one embodiment, the two hybridization probes are designed each with a target specific portion. The first hybridization probe is designed to be substantially complementary to a first target domain of a target polynucleotide (e.g., a polynucleotide fragment) and the second hybridization probe is substantially complementary to a second target domain of a target polynucleotide (e.g., a polynucleotide fragment). In general, each target specific sequence of a hybridization probe is at least about 5 nucleotides long, with sequences of about 15 to 30 being typical and 20 being especially common. In one embodiment, the first and second target domains are directly adjacent, e.g., they have no intervening nucleotides. In this embodiment, at least a first hybridization probe is hybridized to the first target domain and a second hybridization probe is hybridized to the second target domain. If perfect complementarity exists at the junction, a ligation structure is formed such that the two probes can be ligated together to form a ligated probe. If this complementarity does not exist (due to mismatch), no ligation structure is formed and the probes are not ligated together to an appreciable degree. This may be done using heat cycling, to allow the ligated probe to be denatured off the target polynucleotide such that it may serve as a template for further reactions. The method may also be done using three hybridization probes or hybridization probes that are separated by one or more nucleotides, if dNTPs and a polymerase are added (this is sometimes referred to as “Genetic Bit” analysis).

Quantitative PCR and digital PCR can be used to measure the level of a polynucleotide in a sample. Digital Polymerase Chain Reaction (digital PCR, dPCR or dePCR) can be used to directly quantify and clonally amplify nucleic acids including DNA, cDNA or RNA. Digital PCR amplifies nucleic acids by temperature cycling of a nucleic acid molecule with a DNA polymerase. The reaction is typically carried out in the dispersed phase of an emulsion capturing each individual nucleic acid molecule present in a sample within many separate chambers or regions prior to PCR amplification. A count of chambers containing detectable levels of PCR end-product is a direct measure of the absolute nucleic acids quantity.

Quantitative polymerase chain reaction (qPCR) is a modification of the polymerase chain reaction and real-time quantitative PCR are useful for measuring the amount of DNA after each cycle of PCR by use of fluorescent markers or other detectable labels. Quantitative PCR methods use the addition of a competitor RNA (for reverse-transcriptase PCR) or DNA in serial dilutions or co-amplification of an internal control to ensure that the amplification is stopped while in the exponential growth phase.

Modifications of PCR and PCR techniques are routine in the art and there are commercially available kits useful for PCR amplification.

A probe or primer of the disclosure can be associated with a detectable label. A signaling component can include any label that can be detected optically, electronically, radioactively and the like. A nucleic acid analog may serve as the signaling component. By “label” or “detectable label” is meant a moiety that allows detection. In one embodiment, the detection label is a primary label. A primary label is one that can be directly detected, such as a fluorophore. In general, labels fall into three classes: a) isotopic labels, which may be radioactive or heavy isotopes; b) magnetic, electrical, thermal labels; and c) colored or luminescent dyes. Common labels include chromophores or phosphors but are typically fluorescent dyes. Suitable dyes for use in the disclosure include, but are not limited to; fluorescent lanthamide complexes, including those of Europium and Terbium, fluorescein, rhodamine, tetramethylrhodamine, eosin, erythrosin, coumarin, methyl-coumarins, quantum dots (also referred to as “nanocrystals”), pyrene, Malacite green, stilbene, Lucifer Yellow, Cascade Blue™, Texas Red, Cy dyes (Cy3, Cy5, and the like), Alexa dyes, phycoerythin, bodipy, and others described in the 6th Edition of the Molecular Probes Handbook by Richard P. Haugland, hereby expressly incorporated by reference.

Such a detectable label may be a radioactive label or may be a luminescent, fluorescent of enzyme label. Indirect detection processes typically comprise probes covalently labeled with a hapten or ligand such as digoxigenin (DIG) or biotin. In one embodiment, following the hybridization step, the target-probe duplex is detected by an antibody- or streptavidin-enzyme complex. Enzymes commonly used in DNA diagnostics are horseradish peroxidase and alkaline phosphatase. Direct detection methods include the use of fluorophor-labeled oligonucleotides, lanthanide chelate-labeled oligonucleotides or oligonucleotide-enzyme conjugates. Examples of fluorophor labels are fluorescein, rhodamine and phthalocyanine dyes.

It will be understood that embodiments of the invention include probes having fluorescent dye molecules, fluorescent compounds, or other fluorescent moieties. A dye molecule may fluoresce, or be induced to fluoresce upon excitation by application of suitable excitation energy (e.g., electromagnetic energy of suitable wavelength), and may also absorb electromagnetic energy (“quench”) emitted by another dye molecule or fluorescent moiety. Any suitable fluorescent dye molecule, compound or moiety may be used in the practice of the invention. For example, suitable fluorescent dyes, compounds, and other fluorescent moieties include fluorescein, 6-carboxyfluorescein (6-FAM), 2′,4′,1,4,-tetrachlorofluorescein (TET), 2′,4′,5′,7′,1,4-hexachlorofluorescein (HEX), 2′,7′-dimethoxy-4′,5′-dichloro-6-carboxyrhodamine (JOE), 2′-chloro-5′-fluoro-7′,8′-fused phenyl-1,4-dichloro-6-carboxyfluorescein (NED) and 2′-chloro-7′-phenyl-1,4-dichloro-6-carboxyfluorescein (VIC), cyanine dyes (e.g., Cy.sup.3, Cy.sup.5, Cy.sup.9, nitrothiazole blue (NTB)), Cys3, FAM™, tetramethyl-6-carboxyrhodamine (TAMRA), tetrapropano-6-carboxyrhodamine (ROX), dipyrromethene boron fluoride (Bodipy), dichloro-fluorescein, dichloro-rhodamine, fluorescein thiosemicarbazide (FTC), sulforhodamine 101 acid chloride (Texas Red), phycoerythrin, rhodamine, carboxytetramethylrhodamine, 4,6-diamidino-2-phenylindole (DAPI), an indopyras dye, pyrenyloxytrisulfonic acid (Cascade Blue), 514 carboxylic acid (Oregon Green), eosin, erythrosin, pyridyloxazole, benzoxadiazole, aminonapthalene, pyrene, maleimide, a coumarin, 4-fluoro-7-nitrobenofurazan (NBD), 4-amino-N-[3-(vinylsulfonyl)-phenyl]naphthalimide-3,6-disulfonate) (Lucifer Yellow), DABCYL, DABSYL, anthraquinone, malachite green, nitrothiazole, and nitroimidazole compounds, propidium iodide, porphyrins, lanthamide cryptates, lanthamide chelates, derivatives and analogs thereof (e.g., 5-carboxy isomers of fluorescein dyes), and other fluorescent dyes and fluorescent molecules and compounds.

An oligonucleotide according to the methods of the invention may be labeled at the 5′ end or the 3′ end of at least one subunit of the probe. In embodiments, oligonucleotides may be labeled at both the 5′ end and the 3′ end. Alternatively, at least one subunit of the probe may be labeled internally, having at least one, and, in embodiments, more than one, internal label. In embodiments, an oligonucleotide may be labeled at an end and may be labeled internally. The oligonucleotides themselves are synthesized using techniques that are also well known in the art. Methods for preparing oligonucleotides of specific sequence are known in the art, and include, for example, cloning and restriction digest analysis of appropriate sequences and direct chemical synthesis, including, for example, the phosphotriester method described by Narang et al., 1979, Methods in Enzymology, 68:190, the phosphodiester method disclosed by Brown et al., 1979, Methods in Enzymology, 68:109, the diethylphosphoramidate method disclosed in Beaucage et al., 1981, Tetrahedron Letters, 22:1859, and the solid support method disclosed in U.S. Pat. No. 4,458,066, or by other chemical methods using a commercial automated oligonucleotide synthesizer. Modified linkages also may be included, for example phosphorothioates.

Examples of detection modes contemplated for the disclosed methods include, but are not limited to, spectroscopic techniques, such as fluorescence and UV-Vis spectroscopy, scintillation counting, and mass spectroscopy. Complementary to these modes of detection, examples of labels for the purpose of detection and quantitation used in these methods include, but are not limited to, chromophoric labels, scintillation labels, and mass labels. The expression levels of polynucleotides and polypeptides measured using these methods may be normalized to a control established for the purpose of the targeted determination.

Label detection will be based upon the type of label used in the particular assay. Such detection methods are known in the art. For example, radioisotope detection can be performed by autoradiography, scintillation counting or phosphor imaging. For hapten or biotin labels, detection is with an antibody or streptavidin bound to a reporter enzyme such as horseradish peroxidase or alkaline phosphatase, which is then detected by enzymatic means. For fluorophor or lanthanide-chelate labels, fluorescent signals may be measured with spectrofluorimeters with or without time-resolved mode or using automated microtitre plate readers. With enzyme labels, detection is by color or dye deposition (p-nitropheny phosphate or 5-bromo-4-chloro-3-indolyl phosphate/nitroblue tetrazolium for alkaline phosphatase and 3,3′-diaminobenzidine-NiCl₂ for horseradish peroxidase), fluorescence (e.g., 4-methyl umbelliferyl phosphate for alkaline phosphatase) or chemiluminescence (the alkaline phosphatase dioxetane substrates LumiPhos 530 from Lumigen Inc., Detroit Mich., or AMPPD and CSPD from Tropix, Inc.). Chemiluminescent detection may be carried out with X-ray or polaroid film or by using single photon counting luminometers.

The methods, compositions, systems and devices disclosed herein find use in the identification and quantization of a target DNA or RNA polynucleotide in a sample, such as in a pool of sequences including one or more target sequences, which may be unrelated polynucleotides. Quantization of specific nucleic acid samples may be achieved by comparing the total signal (fluorescent or otherwise) obtained during the assay with a standard curve of known polynucleotide target concentrations. Specific examples of applications include the detection of pathogenic viruses through the detection of their biomolecules such as DNA or RNA which are indicative of the presence of said targets. Assays having features of the invention may be used to detect and identify the presence of specific DNA sequences and may be used in assays for diagnosis of many types of infection and disease.

These assays are suitable for use on cell lysates, and contaminated samples as well. Since many clinical samples are rich with contaminants, it is advantageous that the described assays herein work under these conditions. Although many methods are currently available for DNA extraction and purification from tissues, assays such as those disclosed herein (QIAGEN kits, etc.), which are proficient in analyzing and working with contaminated samples, are very valuable and increases the robustness of the assay. For clinical sample use with the disclosed assays, sample preparation kits may be used. For example, samples suspected of containing pathogenic DNA may be used. Exemplary kits and protocols that can be used include the QJAamp MinElute Virus Spin Kit provided by Qiagen. This kit allows DNA isolation from clinical samples in roughly 1 hour. Other methods for sample preparation are available from suppliers such as Promega.

Polynucleotides may be prepared from samples using known techniques. For example, the sample may be treated to lyse a cell comprising the target polynucleotide, using known lysis buffers, sonication techniques, electroporation, and the like. Many methods for cell lysis are common knowledge for those trained in the art.

The following Examples are provided to illustrate and do not limit the invention.

EXAMPLES

The following abbreviations and definitions will assist in understanding aspect of the disclosure and the assays performed.

Ct (Cycle Threshold): Cycle number (in qPCR) at which the fluorescence generated within a reaction well exceeds the defined threshold. The threshold is arbitrarily defined by the qPCR instrument manufacturer to reflect the point during the reaction at which a sufficient number of amplicons have accumulated.

gDNA (genomic DNA): Deoxyribonucleic acid that has been purified from tissue and/or cultured cells.

Percentage Coefficient of Variation (% CV): The coefficient of variation (CV) is a normalized measure of dispersion of a probability distribution. It is defined as the ratio of the standard deviation σ to the mean μ:

$c_{v} = \frac{\sigma}{\mu}$

Slope: The slope or gradient of a line describes its steepness, incline, or grade. An acceptable slope of the linear regression equation for the qPCR should be within the range of −3.00 to −3.7.

R-squared (R²) Value (also known as the Pearson Correlation Coefficient): The correlation of the line, R², is a measure of how well the data fits the model and how well the data fits on a straight line. It is influenced by pipetting accuracy and by the range of the assay. An R² of ≧0.94 is acceptable.

qPCR Percentage Efficiency (% Efficiency): Amplification efficiency, E, is the efficiency of amplification at varying template concentrations and is calculated from the slope of the standard curve using the following formula:

E=10̂(−1/slope)

The % efficiency is the percent of template that was amplified in each cycle and is calculated using the following formula:

% Efficiency=(E−1)×100%

The % efficiency should be between 85% and 115%.

LOD: Limit of detection

LLOQ: Lower limit of quantitation.

ND: Non-detected.

NA: Not applicable.

NTC (Non-template control): A series of reaction wells in a qPCR experiment that contains all the reagents necessary for amplification with elution buffer or water substituted for sample DNA.

qPCR: Real-time quantitative polymerase chain reaction.

Example 1 Design of Primer/Probe Sets

Two primer/probe sets were designed for XMRV specific qPCR:

1. XMRV gag XMRV 628F (SEQ ID NO: 1) (5′-ACTACCCCTCTGAGTCTAACC-3′) XMRV764R (SEQ ID NO: 2) (5′-GGCCATCCTACATTGAAAGTTG-3′) XMRV gag probe (SEQ ID NO: 3) (5′-FAM-CGCATTGCATCCAACCAGTCTGTG-3′-BHQ)

Amplification curves are shown in FIG. 6.

2. XMRV env XMRV 6252F (SEQ ID NO: 4) (5′-TTTGATTCCTCAGTGGGCTC-3′) XMRV6391R (SEQ ID NO: 5) (5′-CGATACAGTCTTAGTCCCCATG-3′) XMRV env probe (SEQ ID NO: 6) (5′-HEX-CCCTTTTACCCGCGTCAGTGAATTCT-3′-BHQ)

Two primer probe sets were designed for detection of all MLV related retroviruses. Amplification curves are shown in FIG. 7.

3. MLV Pol 1 pol-F (SEQ ID NO: 7) (5′-AACAAGCGGGTGGAAGACATC-3′) pol-R (SEQ ID NO: 8) (5′-CAAAGGCGAAGAGAGGCTGAC-3′) pol probe (SEQ ID NO: 9) (5′-HEX-CCCACCGTGCCCAACCCTTACAACC-3′-TAMRA) 4. MLV Pol 2 5′ Pol2 Primer (SEQ ID NO: 10) (CAAGGGGCTACTGGAGGAAAG) 3′ Pol2 Primer: (SEQ ID NO: 11) (CTTTCCTCCATGTACCAGACTG) Pol2 Probe: (SEQ ID NO: 12) (5HEX/TATCGCTGGACCACGGATCGCAA/3BHQ_1)

Two primer probe sets wer designed for detection of amphotropic MLV virus:

5. MLV Env2 5′Env2 primer: (SEQ ID NO: 13) 5′-ACCCTCAACCGCCCCTACAAGT-3′ 3′Env2 primer: (SEQ ID NO: 14) 5′-GTTAAGCGCCTGATAGGCTC-3′ Env2 probe: (SEQ ID NO: 15) 5′-/FAM/CCCCAAATGAAAGACCCCCGCTGACG/BHQ/-3′ 6. MLV LTR: 5′ Primer = MLV-U3-B: (SEQ ID NO: 16) AGC CCA CAA CCC CTC ACT C 3′ Primer = 3-MLV-Psi: (SEQ ID NO: 17) TCT CCC GAT CCC GGA CGA FAM Probe = MLV-U5-Psi: (SEQ ID NO: 18) FAM-CCCCAAATGAAAGACCCCCGCTGACG 3BHQ_1

One primer probe set was designed for detection of a cytosine deaminase (CD) gene.

7. CD: 5′ yCD2 Primer: (SEQ ID NO: 19) (ATC ATC ATG TAC GGC ATC CCT AG) 3′ yCD2 Primer: (SEQ ID NO: 20) (TGA ACT GCT TCA TCA GCT TCT TAC) yCD2 Probe: (SEQ ID NO: 21) (5FAM/TCA TCG TCA ACA ACC ACC ACC TCG T/3BHQ_1)

Oligonucleotides for primer probe sets were ordered from IDT (Integrated DNA Technologies, Inc., San Diego, Calif.).

Example 2 Preparation of Genomic DNA from Blood and Other Tissues from Mammals Including Human and Canines for PCR Testing

The XMRV (xenotropic murine leukemia virus-related virus) qPCR assay is performed to quantify DNA. Total DNA extraction from the specimens samples is generated by standard means such as the use of commercially available kits (QIAGEN DNA blood mini kit, QIAGEN DNA Tissue kit, Promega DNA Tissue Kit, Promega DNA Cell Kit). A quantitation curve is established with 8 non-zero samples comprising of serial dilutions of defined copy number of reference plasmid to generate a Ct value versus copy number correlation. Linear regression analysis generates an equation which is used to calculate the copy number in the sample. Quantitative curves generation are shown for XMRV gag (FIG. 8), XMRV env (FIG. 9), XMRV pol2 (FIG. 10).

Example 3 Preparation of Plasma from Humans and Dogs for RT-PCR Testing

Blood was collected in blood collection tubes, and serum or plasma prepared from the whole blood by conventional means. The XMRV (xenotropic murine leukemia virus-related virus) RT-PCR assay is performed to quantify RNA from biological samples, such as whole blood and plasma, without the need for RNA extraction. The assay employs a two-step amplification process with the initial step consisting of the distribution of 2 μL of experimental sample directly into a cDNA reaction mix. Following completion of the reverse transcriptase (RT) cDNA synthesis, a 2 μL aliquot is removed, transferred into a qPCR reaction mix and a qPCR protocol is performed. A quantitation curve is established with 6 non-zero samples comprising of serial dilutions of defined copy number of reference vector to generate a Ct value versus copy number correlation. Linear regression analysis generates an equation which is used to calculate the copy number in the sample. Quantitative curves generation are shown in FIG. 15.

Example 4 Standardization and Validation of QPCR DNA Assays

A series of experiments were performed as outlined below:

-   1) To optimize the cycling parameters of the quantitative PCR (qPCR)     protocol for XMRV detection including primer and probe     concentrations and annealing temperature. -   2) To assess detection sensitivity in spiked human whole blood     genomic DNA (gDNA) targeted with the XMRV env, XMRV gag and XMRV     pol2 primer/probe sets using qPCR. -   3) To assess the use of an additional set of three pre-cycling steps     (defined as a stage) in the qPCR protocol with respect to detection     sensitivity. -   4) To assess for variance in XMRV detection sensitivity from     independent sources of human whole blood. -   5) To assess for recovery of 22Rv1 XMRV positive control spiked into     human whole blood gDNA.

Assay Design

a. Optimization of Cycling Parameters for the qPCR Protocol.

A matrix of primers and probe were made up in various concentration combinations and were used to target the appropriate XMRV plasmid (pUC57 XMRV gag, pET28b XMRV env or pAZ3-emd pol2) containing the gene of interest. The choice of optimal primer concentrations were made based on comparisons of Ct value, standard deviation and relative fluorescence units (RFU). SYBR Green was used for the primer concentration optimization qPCR assay and TaqMan was used for the probe concentration optimization assay. Annealing temperature optimization was carried out by performing a qPCR annealing temperature gradient ranging from 50° C. to 65° C. Plasmids specific for the gene of interest were targeted with the appropriate XMRV primer sets.

b. Detection Sensitivity in Human Whole Blood gDNA Spiked with Plasmid DNA and Targeted with XMRV Env, XMRV Gag or XMRV Pol2 Primer/Probe Sets Using qPCR.

Genomic DNA extracted from human whole blood was spiked with known copy numbers of plasmid DNA containing the gene of interest. Serial log dilutions of the spiked gDNA were made and qPCR was performed. The samples were targeted with XMRV env (FIG. 9), XMRV gag (FIG. 8) and XMRV pol2 (FIG. 10) primer/probe sets in single qPCR reactions.

c. Detection Sensitivity in Human Whole Blood gDNA Spiked with Plasmid DNA and Targeted with XMRV Env, XMRV Gag or XMRV Pol2 Primer/Probe Sets Using a One-Stage qPCR Protocol.

Human whole blood gDNA was spiked with known copy numbers of plasmid DNA containing the gene of interest. Serial log dilutions of the spiked gDNA were made and a modified version of the qPCR protocol was performed by adding a set of three pre-cycling steps (defined as a one-stage qPCR protocol) to the current qPCR protocol. The samples were targeted with XMRV env (FIG. 9), XMRV gag (FIG. 8) and XMRV pol2 (FIG. 10) primer/probe sets in single qPCR reactions.

d. Assessment of XMRV Detection Sensitivity from Human Whole Blood Sourced from Healthy Donors and Spiked with Plasmid DNA.

Genomic DNA from whole blood from healthy donors were used to spike in known copy numbers of plasmid DNA. Serial dilutions of the gDNA were made to generate 1E3, 1E2, 1E1 and 1E0 copies per reaction. A 0-Stage and a 1-stage qPCR protocol were performed. The samples were targeted with XMRV env (FIG. 12), XMRV gag (FIG. 11) or XMRV pol2 (FIG. 13) primer/probe sets in single qPCR reactions.

e. 22Rv1 Positive Control Recovery Assessment Spiked into Human Whole Blood gDNA.

22Rv1 gDNA (positive for XMRV, E. C. Knouf et al., J. Virol 83:78353-7356 2009) was spiked into purified human whole blood gDNA (pre and post gDNA extraction) at increasing log dilutions (one human whole blood sample control and one TE sample were spiked pre-extraction with 500 ng of 22Rv1 gDNA to yield a final concentration of ˜2.5 ng/μL). A 0-Stage and a 1-stage qPCR protocol were performed with primers targeting the XMRV gag, XMRV env and XMRV pol sequences.

Optimizations (primer concentration and temperature) for Pol primer set were carried out.

Both XMRV gag and XMRV env primer sets are XMRV specific whereas the Pol primer sets detect both MLV and XMRV.

A qPCR protocol used for all 4 primer sets: BioRad Supermix65.prcl

Step 1: 95° C.  5 min Step 2: 95° C. 15 sec Step 3: 65° C. 30 sec [repeat step 2-3 44X more times]

FIGS. 6 and 7 show results obtained by the methods and compositions disclosed above.

TaqqMan® Gold RT-PCR Kit and TaqMan° PCR universal master mix are obtained from PE Biosystems. RNAeasy® mini kit and QIAamp® viral RNA mini kit are obtained from Qiagen. Various cell culture materials and biological samples to be tested are obtained from vendors or subjects.

MLV recombinant isolates comprise the sequences set forth in International Application No. PCT/US09/58512 and published on Apr. 1, 2010 as publication no. WO 2010/036986.

Two primer/probe sets for the detection of XMRV were designed as set forth above. One forward primer (FP), one reverse primer (RP), and one probe were used for the detection of XMRV gag and XMRV env. A third set of primer/probe was used for the detection of XMRV and MLV using the primers above that amplify the pol region of XMRV and MLV.

The qPCR reaction mixture contains 900 nM primers (both forward and reverse) and 200 nM probe. Concentrations tested to be effective for detection include, 100, 200, 300, 400, 500, 600, 700, 800, 900 nM and any ratio between 1:1, 1:2, 1:3, 1:4 of primer concentrations. The activation of Taq polymerase is achieved at 95° C. for 5 minutes is followed by forty-four cycles of denaturation at 95° C. for 15 seconds and annealing and elongation at 65° C. for 30 seconds.

Example 5 Detection of MLV in Formalin Fixed Paraffin Embedded Tissue Samples

Tumors from mice were removed and divided into 2 equal parts. One part of the tumor was formalin-fixed, paraffin-embedded and the other part of the tumor was frozen at −80° C. The FFPE mouse tumor tissue was cut in half, with one half spiked-in with a known copy number amount of pAZ3-emd and the other half was not spiked-in. A known copy number amount of pAZ3-emd was spiked-in to the frozen fresh mouse tissue and pre-processing incubation buffer. The FFPE and frozen fresh mouse tissues were incubated at 56° C. overnight in a pre-processing incubation buffer containing proteinase K and dithiothreitol (DTT). The following day, the mouse tissue was processed on the Maxwell 16 instrument to extract out gDNA as per standard procedure. The extracted gDNA concentration was quantified on the Nanodrop 1000. The extracted DNA was tested for presence of MLV and env2 sequences by qPCR with the results shown in FIG. 14.

Example 6 XMRV/MLV RT-PCR Assay

The XMRV (xenotropic murine leukemia virus-related virus) RT-PCR assay is performed to quantify RNA from biological samples, such as whole blood and plasma, without the need for RNA extraction. The assay employs a two-step amplification process with the initial step consisting of the distribution of 2 μL of experimental sample directly into a cDNA reaction mix. Following completion of the reverse transcriptase (RT) cDNA synthesis, a 2 μL aliquot is removed, transferred into a qPCR reaction mix and a qPCR protocol is performed. A quantitation curve is established with 7 non-zero samples comprising of serial dilutions of defined copy number of reference vector to generate a Ct value versus copy number correlation. Linear regression analysis generates an equation which is used to calculate the copy number in the sample. (FIG. 15).

Four control samples and one reagent control are used for this assay and are run in parallel with all test samples. The two step reaction requires controls for both the RT procedure and the qPCR procedure. Therefore, a positive, a negative and a non-template control are included for the cDNA synthesis step and a positive, negative and non-template control are included for the qPCR portion of the process.

A negative matrix sample (i.e. whole blood) is spiked with a defined quantity of 22Rv1 viral vector (see description under ‘Reference Standard’). This control is prepared fresh with each run to determine the efficiency of the cDNA generation in the RT step.

22Rv1 genomic DNA containing the integrated retroviral vector sequences of XMRV provides the best biophysical mimic of the actual amplification target to be screened in patient tissues.

A negative matrix sample (i.e. whole blood) is used as a negative RT control as it does not contain any detectable XMRV endogenous sequences. This control is prepared fresh with each run to verify that non-specific products are not generated during cDNA synthesis of the qRT step. Confirmation is obtained upon completion of the qPCR procedure. No amplification is expected.

DNA isolated from non-infected U-87 cell is used as a negative control as it does not contain any endogenous sequences detectable by the XMRV primer sets.

The 22Rv1 human prostate carcinoma epithelial cell line has been shown to produce high-titer of the human retrovirus XMRV. This cell line was bought from ATCC and propagated in RPMI-1640 Medium containing 10% FBS, Sodium Pyruvate and Glutamax. The cell line was passaged four times before obtaining the supernatant containing the viral vector. The supernatant was filtered through a 0.45 μm filter and stored at −80° C.

Reference vector 22Rv1 was used to spike PBS for generating a quantitation curve. Known copy numbers of vector were serially diluted to generate a Ct value versus copy number correlation. Linear regression analysis generates an equation which was used to calculate the copy number in the sample. Copy number was determined by a titer analysis which measures the number of copies of the viral genome integrated into the genome of target cells (transduction units, TU). The copy number was measured in TU equivalents.

Several studies were conducted to determine the appropriate primer sets, the optimal concentration for the reactions and the optimal temperature for the cycling parameters. Specific primer sets were designed and tested for human derived material. The goal of these experiments was to identify primer sets that were XMRV specific and did not present background in test samples.

The following primer sets were identified for targeting genes specific for XMRV:

1. XMRV gag XMRV 628F (SEQ ID NO: 1) (5′-ACTACCCCTCTGAGTCTAACC-3′) XMRV764R (SEQ ID NO: 2) (5′-GGCCATCCTACATTGAAAGTTG-3′) XMRV gag probe (SEQ ID NO: 3) (5′-FAM-CGCATTGCATCCAACCAGTCTGTG-3′-BHQ) 2. XMRV env XMRV 6252F (SEQ ID NO: 4) (5′-TTTGATTCCTCAGTGGGCTC-3′) XMRV6391R (SEQ ID NO: 5) (5′-CGATACAGTCTTAGTCCCCATG-3′) XMRV env probe (SEQ ID NO: 6) (5′-HEX-CCCTTTTACCCGCGTCAGTGAATTCT-3′-BHQ)

Two primer probe sets were designed for detection of all MLV related retroviruses and XMRV.

3. MLV Pol 1 pol-F (SEQ ID NO: 7) (5′-AACAAGCGGGTGGAAGACATC-3′) pol-R (SEQ ID NO: 8) (5′-CAAAGGCGAAGAGAGGCTGAC-3′) pol probe (SEQ ID NO: 9) (5′-HEX-CCCACCGTGCCCAACCCTTACAACC-3′-TAMRA) 4. MLV Pol 2 5′ Pol2 Primer (SEQ ID NO: 10) (CAAGGGGCTACTGGAGGAAAG) 3′ Pol2 Primer: (SEQ ID NO: 11) (CTTTCCTCCATGTACCAGACTG) Pol2 Probe: (SEQ ID NO: 12) (5HEX/TATCGCTGGACCACGGATCGCAA/3BHQ_1)

Two primer probe sets were designed for detection of amphotropic MLV virus.

5. MLV Env2 5′Env2 primer: (SEQ ID NO: 13) 5′-ACCCTCAACCGCCCCTACAAGT-3′ 3′Env2 primer: (SEQ ID NO: 14) 5′-GTTAAGCGCCTGATAGGCTC-3′ Env2 probe: (SEQ ID NO: 15) 5′-/FAM/CCCCAAATGAAAGACCCCCGCTGACG/BHQ/-3′ 6. MLV LTR One primer probe set was designed for detection of MLV in the LTR sequence 5′MLVLTR primer: (SEQ ID NO: 16) AGC CCA CAA CCC CTC ACT C 3′ MLVLTR primer (SEQ ID NO: 17) TCT CCC GAT CCC GGA CGA MLVLTR probe: (SEQ ID NO: 18) FAM-CCCCAAATGAAAGACCCCCGCTGACG 3BHQ_1 7. Cytosine deaminase gene One primer probe set was designed for detection of the Cytosine deaminase gene 5′ yCD2 Primer: (SEQ ID NO: 19) (ATC ATC ATG TAC GGC ATC CCT AG) 3′ yCD2 Primer: (SEQ ID NO: 20) (TGA ACT GCT TCA TCA GCT TCT TAC) yCD2 Probe: (SEQ ID NO: 21) (5FAM/TCA TCG TCA ACA ACC ACC ACC TCG T/3BHQ_1).

Example 7 Monitoring of GBM Patients Treated with an MLV Vector

Open-label, ascending-dose trial of the safety and tolerability of increasing doses of Toca 511 administered to subjects with recurrent High Grade Glioma (including GBM) who have undergone surgery followed by adjuvant radiation and chemotherapy was carried out (see http[:]//clinicaltrials.gov/ct2/show/NCT01156584? term=tocagen&rank=1). Ascending doses of Toca 511(aka T5.0002) were prepared suitable for clinical use (WO2010148203) and delivered via stereotactic transcranial injection into the tumor. The starting dose was 2.6×10³ TU/g. Subjects meeting all of the inclusion and none of the exclusion criteria received Toca 511 via stereotactic, transcranial injection into their tumor. Approximately three weeks (±1 week) later subjects underwent a baseline gadolinium-enhanced MRI (Gd-MRI) scan and then began treatment with oral 5-FC at approximately 130 mg/kg/day for 6 days. On the 4th, 5th or 6th day of dosing the trough 5-FC serum concentration was determined and the dose of 5-FC adjusted in subsequent cycles to maintain the trough concentration in the therapeutic range. If tolerated, these 6-day courses of 5-FC were repeated approximately every 4 weeks (±1 week) until institution of new antineoplastic treatment for tumor progression. Subjects undergo Gd-MRI scanning approximately every 8 weeks. Tumor response are assessed using the Macdonald criteria. A standard dose-escalation algorithm is being followed. Three subjects are evaluated at each of up to four dose levels of Toca 511 (2.6×10³, 9.5×10³, 2.5×10⁴, and the Maximum Feasible Dose [MFD], not to exceed 1×105 TU/g). So far three patients at the lowest dose level have been treated. Two patients 101 and 102 were monitored using qPCR testing of whole blood DNA (MLVLTR Primer probe set) and RT-qPCR using the MLV env2 primer-probe set. In addition, saliva an urine were monitored by DNA qPCR, and antibodies to the vector were measured (ref MLV ELISA Application?). These data are shown in FIG. 16.

Other primers useful in the methods and composition of the disclosure for detecting XMRV and MLV related viruses include those in Table 1.

TABLE 1 Sequence Product Product 5 XMRV 3 XMRV Definition Pair Rating Length Tm Sense Primer Anti-sense Primer position position XMRV 1581-1778 66.8 178 78.2 AGGTAGGAACCACCTAGTCC AGGGTCATAAGGAGTGTACC 1581 1758 XMRV 1581-1778 63.6 168 78.3 AGGTAGGAACCACCTAGTCC GGAGTGTACCTGCGATAGGC 1581 1748 XMRV 1581-1778 63.5 198 78.9 AGGTAGGAACCACCTAGTCC GTTTCTTGCCCTGGGTCCTC 1581 1778 XMRV 1581-1778 62.5 188 78.8 AGGTAGGAACCACCTAGTCC CTGGGTCCTCAGGGTCATAA 1581 1768 XMRV 1581-1778 60.1 173 78 AGGTAGGAACCACCTAGTCC CATAAGGAGTGTACCTGCGA 1581 1753 XMRV 1729-1948 73.3 195 75.8 TCGCAGGTACACTCCTTATG TCTCTTTCTTCCGGGGTTTC 1734 1928 XMRV 1729-1948 69.8 215 76 TCGCAGGTACACTCCTTATG TTTCTCTCCTGATACGTTCC 1734 1948 XMRV 1729-1948 69 200 76 TCGCAGGTACACTCCTTATG GTTCCTCTCTTTCTTCCGGG 1734 1933 XMRV 1729-1948 68.2 200 76 GCCTATCGCAGGTACACTCC TCTCTTTCTTCCGGGGTTTC 1729 1928 XMRV 1729-1948 66 205 76.2 GCCTATCGCAGGTACACTCC GTTCCTCTCTTTCTTCCGGG 1729 1933 XMRV 1729-1948 66 210 76.2 TCGCAGGTACACTCCTTATG CTCCTGATACGTTCCTCTCT 1734 1943 XMRV 1729-1948 63.8 180 75.1 TTATGACCCTGAGGACCCAG TCTCTTTCTTCCGGGGTTTC 1749 1928 XMRV 1729-1948 61.8 200 75.4 TTATGACCCTGAGGACCCAG TTTCTCTCCTGATACGTTCC 1749 1948 XMRV 1729-1948 61.4 210 75.8 GGTACACTCCTTATGACCCT TTTCTCTCCTGATACGTTCC 1739 1948 XMRV 1729-1948 61.1 185 75.3 TTATGACCCTGAGGACCCAG GTTCCTCTCTTTCTTCCGGG 1749 1933

Table 2 provides additional primer pairs and probes that are useful in the methods and compositions of the disclosure, for example for quantitative PCR and quantitative RT-PCR, and useful for XMRV or XMRV and MLV related virus detection:

TABLE 2 Detects MLV 5′ XMRV 3′ XMRV related Probe Product Anti-sense coor- coor- and Sequence Rating Sequence Tm GC % Length Sense Primer Primer dinate dinate XMRV XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 106 CTATAAAGTCCAAAC GAGGAAGGTTGT 1015 1121 no CTCATTGACCTT CTCCTAAGCC GCTCCGTAC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 114 TCTATAAAGTCCAAA GGCAGAGGAGGA 1015 1128 no TCATTGACCTTC CCTCCTAAGC AGGTTGTG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 114 TCTATAAAGTCCAAA GGCAGAGGAGGA 1015 1128 no TCATTGACCTT CCTCCTAAGC AGGTTGTG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 114 TCTATAAAGTCCAAA GGCAGAGGAGGA 1015 1128 no CTCATTGACCTT CCTCCTAAGC AGGTTGTG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 114 TCTATAAAGTCCAAA GGCAGAGGAGGA 1015 1128 no TCATTGACCT CCTCCTAAGC AGGTTGTG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 114 TCTATAAAGTCCAAA GGCAGAGGAGGA 1015 1128 no TCTCATTGACCT CCTCCTAAGC AGGTTGTG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 114 TCTATAAAGTCCAAA GGCAGAGGAGGA 1015 1128 no CTCATTGACCT CCTCCTAAGC AGGTTGTG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 129 TCTATAAAGTCCAAA TTCATTGTTCTCCC 1015 1143 no TCATTGACCTTC CCTCCTAAGC TGGCAGAG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 129 TCTATAAAGTCCAAA TTCATTGTTCTCCC 1015 1143 no TCATTGACCTT CCTCCTAAGC TGGCAGAG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 129 TCTATAAAGTCCAAA TTCATTGTTCTCCC 1015 1143 no CTCATTGACCTT CCTCCTAAGC TGGCAGAG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 129 TCTATAAAGTCCAAA TTCATTGTTCTCCC 1015 1143 no TCATTGACCT CCTCCTAAGC TGGCAGAG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 129 TCTATAAAGTCCAAA TTCATTGTTCTCCC 1015 1143 no TCTCATTGACCT CCTCCTAAGC TGGCAGAG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 129 TCTATAAAGTCCAAA TTCATTGTTCTCCC 1015 1143 no CTCATTGACCT CCTCCTAAGC TGGCAGAG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 139 TCTATAAAGTCCAAA CCGCCTCTTCTTCA 1015 1153 no TCATTGACCTTC CCTCCTAAGC TTGTTCTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 139 TCTATAAAGTCCAAA CCGCCTCTTCTTCA 1015 1153 no TCATTGACCTT CCTCCTAAGC TTGTTCTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 139 TCTATAAAGTCCAAA CCGCCTCTTCTTCA 1015 1153 no CTCATTGACCTT CCTCCTAAGC TTGTTCTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 139 TCTATAAAGTCCAAA CCGCCTCTTCTTCA 1015 1153 no TCATTGACCT CCTCCTAAGC TTGTTCTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 139 TCTATAAAGTCCAAA CCGCCTCTTCTTCA 1015 1153 no TCTCATTGACCT CCTCCTAAGC TTGTTCTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 139 TCTATAAAGTCCAAA CCGCCTCTTCTTCA 1015 1153 no CTCATTGACCT CCTCCTAAGC TTGTTCTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 140 TCTATAAAGTCCAAA GCCGCCTCTTCTTC 1015 1154 no TCATTGACCTTC CCTCCTAAGC ATTGTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 140 TCTATAAAGTCCAAA GCCGCCTCTTCTTC 1015 1154 no TCATTGACCTT CCTCCTAAGC ATTGTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 140 TCTATAAAGTCCAAA GCCGCCTCTTCTTC 1015 1154 no CTCATTGACCTT CCTCCTAAGC ATTGTTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 140 TCTATAAAGTCCAAA GCCGCCTCTTCTTC 1015 1154 no TCATTGACCT CCTCCTAAGC ATTGTTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 140 TCTATAAAGTCCAAA GCCGCCTCTTCTTC 1015 1154 no TCTCATTGACCT CCTCCTAAGC ATTGTTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 140 TCTATAAAGTCCAAA GCCGCCTCTTCTTC 1015 1154 no CTCATTGACCT CCTCCTAAGC ATTGTTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 142 TCTATAAAGTCCAAA TGGCCGCCTCTTCT 1015 1156 no TCATTGACCTTC CCTCCTAAGC TCATTG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 142 TCTATAAAGTCCAAA TGGCCGCCTCTTCT 1015 1156 no TCATTGACCTT CCTCCTAAGC TCATTG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 142 TCTATAAAGTCCAAA TGGCCGCCTCTTCT 1015 1156 no CTCATTGACCTT CCTCCTAAGC TCATTG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 142 TCTATAAAGTCCAAA TGGCCGCCTCTTCT 1015 1156 no TCATTGACCT CCTCCTAAGC TCATTG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 142 TCTATAAAGTCCAAA TGGCCGCCTCTTCT 1015 1156 no TCTCATTGACCT CCTCCTAAGC TCATTG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 142 TCTATAAAGTCCAAA TGGCCGCCTCTTCT 1015 1156 no CTCATTGACCT CCTCCTAAGC TCATTG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 144 TCTATAAAGTCCAAA GGTGGCCGCCTCT 1015 1158 no TCATTGACCTTC CCTCCTAAGC TCTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 144 TCTATAAAGTCCAAA GGTGGCCGCCTCT 1015 1158 no TCATTGACCTT CCTCCTAAGC TCTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 144 TCTATAAAGTCCAAA GGTGGCCGCCTCT 1015 1158 no CTCATTGACCTT CCTCCTAAGC TCTTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 144 TCTATAAAGTCCAAA GGTGGCCGCCTCT 1015 1158 no TCATTGACCT CCTCCTAAGC TCTTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 144 TCTATAAAGTCCAAA GGTGGCCGCCTCT 1015 1158 no TCTCATTGACCT CCTCCTAAGC TCTTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 144 TCTATAAAGTCCAAA GGTGGCCGCCTCT 1015 1158 no CTCATTGACCT CCTCCTAAGC TCTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 188 CTATAAAGTCCAAAC CCGCAGTCGAGAC 1015 1203 no CTCATTGACCTT CTCCTAAGCC ACCATG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 191 CTATAAAGTCCAAAC TCCCCGCAGTCGA 1015 1206 no TCATTGACCTTC CTCCTAAGCC GACAC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 191 CTATAAAGTCCAAAC TCCCCGCAGTCGA 1015 1206 no CTCATTGACCTT CTCCTAAGCC GACAC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 194 TCTATAAAGTCCAAA CTTCCCCGCAGTC 1015 1208 no TCATTGACCTTC CCTCCTAAGC GAGAC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 194 TCTATAAAGTCCAAA CTTCCCCGCAGTC 1015 1208 no TCATTGACCTT CCTCCTAAGC GAGAC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 194 TCTATAAAGTCCAAA CTTCCCCGCAGTC 1015 1208 no CTCATTGACCTT CCTCCTAAGC GAGAC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 194 TCTATAAAGTCCAAA CTTCCCCGCAGTC 1015 1208 no TCATTGACCT CCTCCTAAGC GAGAC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 194 TCTATAAAGTCCAAA CTTCCCCGCAGTC 1015 1208 no TCTCATTGACCT CCTCCTAAGC GAGAC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 194 TCTATAAAGTCCAAA CTTCCCCGCAGTC 1015 1208 no CTCATTGACCT CCTCCTAAGC GAGAC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 199 CTATAAAGTCCAAAC TCTCTCCTTCCCCG 1015 1214 no TCATTGACCTTC CTCCTAAGCC CAGTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 199 CTATAAAGTCCAAAC TCTCTCCTTCCCCG 1015 1214 no CTCATTGACCTT CTCCTAAGCC CAGTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 199 CTATAAAGTCCAAAC TCTCTCCTTCCCCG 1015 1214 no CTCATTGACCT CTCCTAAGCC CAGTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 106 CTATAAAGTCCAAAC GAGGAAGGTTGT 1016 1121 no TCATTGACCTTC CTCCTAAGCC GCTCCGTAC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 106 CTATAAAGTCCAAAC GAGGAAGGTTGT 1016 1121 no TCATTGACCTT CTCCTAAGCC GCTCCGTAC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 106 CTATAAAGTCCAAAC GAGGAAGGTTGT 1016 1121 no TCATTGACCT CTCCTAAGCC GCTCCGTAC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 106 CTATAAAGTCCAAAC GAGGAAGGTTGT 1016 1121 no TCTCATTGACCT CTCCTAAGCC GCTCCGTAC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 106 CTATAAAGTCCAAAC GAGGAAGGTTGT 1016 1121 no CTCATTGACCT CTCCTAAGCC GCTCCGTAC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 111 CTATAAAGTCCAAAC CAGAGGAGGAAG 1016 1126 no TCATTGACCTTC CTCCTAAGCC GTTGTGCTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 111 CTATAAAGTCCAAAC CAGAGGAGGAAG 1016 1126 no TCATTGACCTT CTCCTAAGCC GTTGTGCTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 111 CTATAAAGTCCAAAC CAGAGGAGGAAG 1016 1126 no CTCATTGACCTT CTCCTAAGCC GTTGTGCTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 111 CTATAAAGTCCAAAC CAGAGGAGGAAG 1016 1126 no TCATTGACCT CTCCTAAGCC GTTGTGCTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 111 CTATAAAGTCCAAAC CAGAGGAGGAAG 1016 1126 no TCTCATTGACCT CTCCTAAGCC GTTGTGCTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 111 CTATAAAGTCCAAAC CAGAGGAGGAAG 1016 1126 no CTCATTGACCT CTCCTAAGCC GTTGTGCTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 188 CTATAAAGTCCAAAC CCGCAGTCGAGAC 1016 1203 no TCATTGACCTTC CTCCTAAGCC ACCATG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 188 CTATAAAGTCCAAAC CCGCAGTCGAGAC 1016 1203 no TCATTGACCTT CTCCTAAGCC ACCATG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 188 CTATAAAGTCCAAAC CCGCAGTCGAGAC 1016 1203 no TCATTGACCT CTCCTAAGCC ACCATG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 188 CTATAAAGTCCAAAC CCGCAGTCGAGAC 1016 1203 no TCTCATTGACCT CTCCTAAGCC ACCATG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 188 CTATAAAGTCCAAAC CCGCAGTCGAGAC 1016 1203 no CTCATTGACCT CTCCTAAGCC ACCATG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 191 CTATAAAGTCCAAAC TCCCCGCAGTCGA 1016 1206 no TCATTGACCTT CTCCTAAGCC GACAC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 191 CTATAAAGTCCAAAC TCCCCGCAGTCGA 1016 1206 no TCATTGACCT CTCCTAAGCC GACAC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 191 CTATAAAGTCCAAAC TCCCCGCAGTCGA 1016 1206 no TCTCATTGACCT CTCCTAAGCC GACAC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 191 CTATAAAGTCCAAAC TCCCCGCAGTCGA 1016 1206 no CTCATTGACCT CTCCTAAGCC GACAC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 195 CTATAAAGTCCAAAC TCCTTCCCCGCAGT 1016 1210 no TCATTGACCTTC CTCCTAAGCC CGAG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 195 CTATAAAGTCCAAAC TCCTTCCCCGCAGT 1016 1210 no TCATTGACCTT CTCCTAAGCC CGAG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 195 CTATAAAGTCCAAAC TCCTTCCCCGCAGT 1016 1210 no CTCATTGACCTT CTCCTAAGCC CGAG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 195 CTATAAAGTCCAAAC TCCTTCCCCGCAGT 1016 1210 no TCATTGACCT CTCCTAAGCC CGAG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 195 CTATAAAGTCCAAAC TCCTTCCCCGCAGT 1016 1210 no TCTCATTGACCT CTCCTAAGCC CGAG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 195 CTATAAAGTCCAAAC TCCTTCCCCGCAGT 1016 1210 no CTCATTGACCT CTCCTAAGCC CGAG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 199 CTATAAAGTCCAAAC TCTCTCCTTCCCCG 1016 1214 no TCATTGACCTT CTCCTAAGCC CAGTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 199 CTATAAAGTCCAAAC TCTCTCCTTCCCCG 1016 1214 no TCATTGACCT CTCCTAAGCC CAGTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 199 CTATAAAGTCCAAAC TCTCTCCTTCCCCG 1016 1214 no TCTCATTGACCT CTCCTAAGCC CAGTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 127 TATAAAGTCCAAACC TTCATTGTTCTCCC 1017 1143 no TCATTGACCTTC TCCTAAGCC TGGCAGAG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 127 TATAAAGTCCAAACC TTCATTGTTCTCCC 1017 1143 no TCATTGACCTT TCCTAAGCC TGGCAGAG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 127 TATAAAGTCCAAACC TTCATTGTTCTCCC 1017 1143 no CTCATTGACCTT TCCTAAGCC TGGCAGAG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 127 TATAAAGTCCAAACC TTCATTGTTCTCCC 1017 1143 no TCATTGACCT TCCTAAGCC TGGCAGAG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 127 TATAAAGTCCAAACC TTCATTGTTCTCCC 1017 1143 no TCTCATTGACCT TCCTAAGCC TGGCAGAG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 127 TATAAAGTCCAAACC TTCATTGTTCTCCC 1017 1143 no CTCATTGACCT TCCTAAGCC TGGCAGAG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 137 TATAAAGTCCAAACC CCGCCTCTTCTTCA 1017 1153 no TCATTGACCTTC TCCTAAGCC TTGTTCTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 137 TATAAAGTCCAAACC CCGCCTCTTCTTCA 1017 1153 no TCATTGACCTT TCCTAAGCC TTGTTCTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 137 TATAAAGTCCAAACC CCGCCTCTTCTTCA 1017 1153 no CTCATTGACCTT TCCTAAGCC TTGTTCTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 137 TATAAAGTCCAAACC CCGCCTCTTCTTCA 1017 1153 no TCATTGACCT TCCTAAGCC TTGTTCTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 137 TATAAAGTCCAAACC CCGCCTCTTCTTCA 1017 1153 no TCTCATTGACCT TCCTAAGCC TTGTTCTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 137 TATAAAGTCCAAACC CCGCCTCTTCTTCA 1017 1153 no CTCATTGACCT TCCTAAGCC TTGTTCTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 138 TATAAAGTCCAAACC GCCGCCTCTTCTTC 1017 1154 no TCATTGACCTTC TCCTAAGCC ATTGTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 138 TATAAAGTCCAAACC GCCGCCTCTTCTTC 1017 1154 no TCATTGACCTT TCCTAAGCC ATTGTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 138 TATAAAGTCCAAACC GCCGCCTCTTCTTC 1017 1154 no CTCATTGACCTT TCCTAAGCC ATTGTTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 138 TATAAAGTCCAAACC GCCGCCTCTTCTTC 1017 1154 no TCATTGACCT TCCTAAGCC ATTGTTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 138 TATAAAGTCCAAACC GCCGCCTCTTCTTC 1017 1154 no TCTCATTGACCT TCCTAAGCC ATTGTTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 138 TATAAAGTCCAAACC GCCGCCTCTTCTTC 1017 1154 no CTCATTGACCT TCCTAAGCC ATTGTTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 140 TATAAAGTCCAAACC TGGCCGCCTCTTCT 1017 1156 no TCATTGACCTTC TCCTAAGCC TCATTG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 140 TATAAAGTCCAAACC TGGCCGCCTCTTCT 1017 1156 no TCATTGACCTT TCCTAAGCC TCATTG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 140 TATAAAGTCCAAACC TGGCCGCCTCTTCT 1017 1156 no CTCATTGACCTT TCCTAAGCC TCATTG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 140 TATAAAGTCCAAACC TGGCCGCCTCTTCT 1017 1156 no TCATTGACCT TCCTAAGCC TCATTG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 140 TATAAAGTCCAAACC TGGCCGCCTCTTCT 1017 1156 no TCTCATTGACCT TCCTAAGCC TCATTG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 140 TATAAAGTCCAAACC TGGCCGCCTCTTCT 1017 1156 no CTCATTGACCT TCCTAAGCC TCATTG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 142 TATAAAGTCCAAACC GGTGGCCGCCTCT 1017 1158 no TCATTGACCTTC TCCTAAGCC TCTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 142 TATAAAGTCCAAACC GGTGGCCGCCTCT 1017 1158 no TCATTGACCTT TCCTAAGCC TCTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 142 TATAAAGTCCAAACC GGTGGCCGCCTCT 1017 1158 no CTCATTGACCTT TCCTAAGCC TCTTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 142 TATAAAGTCCAAACC GGTGGCCGCCTCT 1017 1158 no TCATTGACCT TCCTAAGCC TCTTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 142 TATAAAGTCCAAACC GGTGGCCGCCTCT 1017 1158 no TCTCATTGACCT TCCTAAGCC TCTTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 142 TATAAAGTCCAAACC GGTGGCCGCCTCT 1017 1158 no CTCATTGACCT TCCTAAGCC TCTTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 186 ATAAAGTCCAAACCT CCGCAGTCGAGAC 1018 1203 no TCATTGACCTTC CCTAAGCC ACCATG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 186 ATAAAGTCCAAACCT CCGCAGTCGAGAC 1018 1203 no TCATTGACCTT CCTAAGCC ACCATG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 186 ATAAAGTCCAAACCT CCGCAGTCGAGAC 1018 1203 no CTCATTGACCTT CCTAAGCC ACCATG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 186 ATAAAGTCCAAACCT CCGCAGTCGAGAC 1018 1203 no TCATTGACCT CCTAAGCC ACCATG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 186 ATAAAGTCCAAACCT CCGCAGTCGAGAC 1018 1203 no TCTCATTGACCT CCTAAGCC ACCATG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 186 ATAAAGTCCAAACCT CCGCAGTCGAGAC 1018 1203 no CTCATTGACCT CCTAAGCC ACCATG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 197 ATAAAGTCCAAACCT TCTCTCCTTCCCCG 1018 1214 no TCATTGACCTTC CCTAAGCC CAGTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 197 ATAAAGTCCAAACCT TCTCTCCTTCCCCG 1018 1214 no TCATTGACCTT CCTAAGCC CAGTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 197 ATAAAGTCCAAACCT TCTCTCCTTCCCCG 1018 1214 no CTCATTGACCTT CCTAAGCC CAGTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 197 ATAAAGTCCAAACCT TCTCTCCTTCCCCG 1018 1214 no TCATTGACCT CCTAAGCC CAGTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 197 ATAAAGTCCAAACCT TCTCTCCTTCCCCG 1018 1214 no TCTCATTGACCT CCTAAGCC CAGTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 197 ATAAAGTCCAAACCT TCTCTCCTTCCCCG 1018 1214 no CTCATTGACCT CCTAAGCC CAGTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 135 TAAAGTCCAAACCTC CCGCCTCTTCTTCA 1019 1153 no TCATTGACCTTC CTAAGCC TTGTTCTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 135 TAAAGTCCAAACCTC CCGCCTCTTCTTCA 1019 1153 no TCATTGACCTT CTAAGCC TTGTTCTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 135 TAAAGTCCAAACCTC CCGCCTCTTCTTCA 1019 1153 no CTCATTGACCTT CTAAGCC TTGTTCTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 135 TAAAGTCCAAACCTC CCGCCTCTTCTTCA 1019 1153 no TCATTGACCT CTAAGCC TTGTTCTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 135 TAAAGTCCAAACCTC CCGCCTCTTCTTCA 1019 1153 no TCTCATTGACCT CTAAGCC TTGTTCTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 135 TAAAGTCCAAACCTC CCGCCTCTTCTTCA 1019 1153 no CTCATTGACCT CTAAGCC TTGTTCTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 136 TAAAGTCCAAACCTC GCCGCCTCTTCTTC 1019 1154 no TCATTGACCTTC CTAAGCC ATTGTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 136 TAAAGTCCAAACCTC GCCGCCTCTTCTTC 1019 1154 no TCATTGACCTT CTAAGCC ATTGTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 136 TAAAGTCCAAACCTC GCCGCCTCTTCTTC 1019 1154 no CTCATTGACCTT CTAAGCC ATTGTTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 136 TAAAGTCCAAACCTC GCCGCCTCTTCTTC 1019 1154 no TCATTGACCT CTAAGCC ATTGTTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 136 TAAAGTCCAAACCTC GCCGCCTCTTCTTC 1019 1154 no CTCATTGACCT CTAAGCC ATTGTTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 140 TAAAGTCCAAACCTC GGTGGCCGCCTCT 1019 1158 no TCATTGACCTTC CTAAGCC TCTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 140 TAAAGTCCAAACCTC GGTGGCCGCCTCT 1019 1158 no TCATTGACCTT CTAAGCC TCTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 140 TAAAGTCCAAACCTC GGTGGCCGCCTCT 1019 1158 no CTCATTGACCTT CTAAGCC TCTTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 140 TAAAGTCCAAACCTC GGTGGCCGCCTCT 1019 1158 no TCATTGACCT CTAAGCC TCTTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 136 TAAAGTCCAAACCTC GCCGCCTCTTCTTC 1019 1158 no TCTCATTGACCT CTAAGCC ATTGTTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 140 TAAAGTCCAAACCTC GGTGGCCGCCTCT 1019 1158 no TCTCATTGACCT CTAAGCC TCTTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 140 TAAAGTCCAAACCTC GGTGGCCGCCTCT 1019 1158 no CTCATTGACCT CTAAGCC TCTTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 92 CCTCCTAAGCCCCAG GAGGAAGGTTGT 1030 1121 no TCATTGACCTTC GTTCTC GCTCCGTAC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 92 CCTCCTAAGCCCCAG GAGGAAGGTTGT 1030 1121 no TCATTGACCTT GTTCTC GCTCCGTAC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 92 CCTCCTAAGCCCCAG GAGGAAGGTTGT 1030 1121 no CTCATTGACCTT GTTCTC GCTCCGTAC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 92 CCTCCTAAGCCCCAG GAGGAAGGTTGT 1030 1121 no TCATTGACCT GTTCTC GCTCCGTAC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 92 CCTCCTAAGCCCCAG GAGGAAGGTTGT 1030 1121 no TCTCATTGACCT GTTCTC GCTCCGTAC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 92 CCTCCTAAGCCCCAG GAGGAAGGTTGT 1030 1121 no CTCATTGACCT GTTCTC GCTCCGTAC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 99 CCTCCTAAGCCCCAG GGCAGAGGAGGA 1030 1128 no TCATTGACCTTC GTTCTC AGGTTGTG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 99 CCTCCTAAGCCCCAG GGCAGAGGAGGA 1030 1128 no TCATTGACCTT GTTCTC AGGTTGTG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 99 CCTCCTAAGCCCCAG GGCAGAGGAGGA 1030 1128 no CTCATTGACCTT GTTCTC AGGTTGTG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 99 CCTCCTAAGCCCCAG GGCAGAGGAGGA 1030 1128 no TCATTGACCT GTTCTC AGGTTGTG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 99 CCTCCTAAGCCCCAG GGCAGAGGAGGA 1030 1128 no TCTCATTGACCT GTTCTC AGGTTGTG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 99 CCTCCTAAGCCCCAG GGCAGAGGAGGA 1030 1128 no CTCATTGACCT GTTCTC AGGTTGTG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 114 CCTCCTAAGCCCCAG TTCATTGTTCTCCC 1030 1143 no TCATTGACCTTC GTTCTC TGGCAGAG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 114 CCTCCTAAGCCCCAG TTCATTGTTCTCCC 1030 1143 no TCATTGACCTT GTTCTC TGGCAGAG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 114 CCTCCTAAGCCCCAG TTCATTGTTCTCCC 1030 1143 no CTCATTGACCTT GTTCTC TGGCAGAG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 114 CCTCCTAAGCCCCAG TTCATTGTTCTCCC 1030 1143 no TCATTGACCT GTTCTC TGGCAGAG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 114 CCTCCTAAGCCCCAG TTCATTGTTCTCCC 1030 1143 no TCTCATTGACCT GTTCTC TGGCAGAG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 124 CCTCCTAAGCCCCAG CCGCCTCTTCTTCA 1030 1153 no TCATTGACCTTC GTTCTC TTGTTCTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 124 CCTCCTAAGCCCCAG CCGCCTCTTCTTCA 1030 1153 no TCATTGACCTT GTTCTC TTGTTCTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 124 CCTCCTAAGCCCCAG CCGCCTCTTCTTCA 1030 1153 no CTCATTGACCTT GTTCTC TTGTTCTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 124 CCTCCTAAGCCCCAG CCGCCTCTTCTTCA 1030 1153 no TCATTGACCT GTTCTC TTGTTCTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 124 CCTCCTAAGCCCCAG CCGCCTCTTCTTCA 1030 1153 no TCTCATTGACCT GTTCTC TTGTTCTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 124 CCTCCTAAGCCCCAG CCGCCTCTTCTTCA 1030 1153 no CTCATTGACCT GTTCTC TTGTTCTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 125 CCTCCTAAGCCCCAG GCCGCCTCTTCTTC 1030 1154 no TCATTGACCTTC GTTCTC ATTGTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 125 CCTCCTAAGCCCCAG GCCGCCTCTTCTTC 1030 1154 no TCATTGACCTT GTTCTC ATTGTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 125 CCTCCTAAGCCCCAG GCCGCCTCTTCTTC 1030 1154 no CTCATTGACCTT GTTCTC ATTGTTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 125 CCTCCTAAGCCCCAG GCCGCCTCTTCTTC 1030 1154 no TCATTGACCT GTTCTC ATTGTTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 125 CCTCCTAAGCCCCAG GCCGCCTCTTCTTC 1030 1154 no TCTCATTGACCT GTTCTC ATTGTTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 125 CCTCCTAAGCCCCAG GCCGCCTCTTCTTC 1030 1154 no CTCATTGACCT GTTCTC ATTGTTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 127 CCTCCTAAGCCCCAG TGGCCGCCTCTTCT 1030 1156 no TCATTGACCTTC GTTCTC TCATTG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 127 CCTCCTAAGCCCCAG TGGCCGCCTCTTCT 1030 1156 no TCATTGACCTT GTTCTC TCATTG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 127 CCTCCTAAGCCCCAG TGGCCGCCTCTTCT 1030 1156 no CTCATTGACCTT GTTCTC TCATTG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 127 CCTCCTAAGCCCCAG TGGCCGCCTCTTCT 1030 1156 no TCATTGACCT GTTCTC TCATTG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 127 CCTCCTAAGCCCCAG TGGCCGCCTCTTCT 1030 1156 no TCTCATTGACCT GTTCTC TCATTG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 127 CCTCCTAAGCCCCAG TGGCCGCCTCTTCT 1030 1156 no CTCATTGACCT GTTCTC TCATTG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 132 CCTCCTAAGCCCCAG GGTGGTGGCCGCC 1030 1158 no TCATTGACCTTC GTTCTC TCTTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 129 CCTCCTAAGCCCCAG GGTGGCCGCCTCT 1030 1158 no TCATTGACCTTC GTTCTC TCTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 132 CCTCCTAAGCCCCAG GGTGGTGGCCGCC 1030 1158 no TCATTGACCTT GTTCTC TCTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 129 CCTCCTAAGCCCCAG GGTGGCCGCCTCT 1030 1158 no TCATTGACCTT GTTCTC TCTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 132 CCTCCTAAGCCCCAG GGTGGTGGCCGCC 1030 1158 no CTCATTGACCTT GTTCTC TCTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 129 CCTCCTAAGCCCCAG GGTGGCCGCCTCT 1030 1158 no CTCATTGACCTT GTTCTC TCTTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 132 CCTCCTAAGCCCCAG GGTGGTGGCCGCC 1030 1158 no TCATTGACCT GTTCTC TCTTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 129 CCTCCTAAGCCCCAG GGTGGCCGCCTCT 1030 1158 no TCATTGACCT GTTCTC TCTTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 132 CCTCCTAAGCCCCAG GGTGGTGGCCGCC 1030 1158 no TCTCATTGACCT GTTCTC TCTTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 129 CCTCCTAAGCCCCAG GGTGGCCGCCTCT 1030 1158 no TCTCATTGACCT GTTCTC TCTTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 132 CCTCCTAAGCCCCAG GGTGGTGGCCGCC 1030 1158 no CTCATTGACCT GTTCTC TCTTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 129 CCTCCTAAGCCCCAG GGTGGCCGCCTCT 1030 1158 no CTCATTGACCT GTTCTC TCTTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 174 CCTCCTAAGCCCCAG CCGCAGTCGAGAC 1030 1203 no TCATTGACCTTC GTTCTC ACCATG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 174 CCTCCTAAGCCCCAG CCGCAGTCGAGAC 1030 1203 no TCATTGACCTT GTTCTC ACCATG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 174 CCTCCTAAGCCCCAG CCGCAGTCGAGAC 1030 1203 no CTCATTGACCTT GTTCTC ACCATG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 174 CCTCCTAAGCCCCAG CCGCAGTCGAGAC 1030 1203 no TCATTGACCT GTTCTC ACCATG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 174 CCTCCTAAGCCCCAG CCGCAGTCGAGAC 1030 1203 no TCTCATTGACCT GTTCTC ACCATG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 174 CCTCCTAAGCCCCAG CCGCAGTCGAGAC 1030 1203 no CTCATTGACCT GTTCTC ACCATG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 177 CCTCCTAAGCCCCAG TCCCCGCAGTCGA 1030 1206 no TCATTGACCTTC GTTCTC GACAC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 177 CCTCCTAAGCCCCAG TCCCCGCAGTCGA 1030 1206 no TCATTGACCTT GTTCTC GACAC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 177 CCTCCTAAGCCCCAG TCCCCGCAGTCGA 1030 1206 no CTCATTGACCTT GTTCTC GACAC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 177 CCTCCTAAGCCCCAG TCCCCGCAGTCGA 1030 1206 no TCATTGACCT GTTCTC GACAC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 177 CCTCCTAAGCCCCAG TCCCCGCAGTCGA 1030 1206 no TCTCATTGACCT GTTCTC GACAC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 177 CCTCCTAAGCCCCAG TCCCCGCAGTCGA 1030 1206 no CTCATTGACCT GTTCTC GACAC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 181 CCTCCTAAGCCCCAG TCCTTCCCCGCAGT 1030 1210 no TCATTGACCTTC GTTCTC CGAG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 181 CCTCCTAAGCCCCAG TCCTTCCCCGCAGT 1030 1210 no TCATTGACCTT GTTCTC CGAG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 181 CCTCCTAAGCCCCAG TCCTTCCCCGCAGT 1030 1210 no CTCATTGACCTT GTTCTC CGAG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 181 CCTCCTAAGCCCCAG TCCTTCCCCGCAGT 1030 1210 no TCATTGACCT GTTCTC CGAG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 181 CCTCCTAAGCCCCAG TCCTTCCCCGCAGT 1030 1210 no TCTCATTGACCT GTTCTC CGAG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 114 CCTCCTAAGCCCCAG TTCATTGTTCTCCC 1030 1210 no CTCATTGACCT GTTCTC TGGCAGAG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 181 CCTCCTAAGCCCCAG TCCTTCCCCGCAGT 1030 1210 no CTCATTGACCT GTTCTC CGAG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 185 CCTCCTAAGCCCCAG TCTCTCCTTCCCCG 1030 1214 no TCATTGACCTTC GTTCTC CAGTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 185 CCTCCTAAGCCCCAG TCTCTCCTTCCCCG 1030 1214 no TCATTGACCTT GTTCTC CAGTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 185 CCTCCTAAGCCCCAG TCTCTCCTTCCCCG 1030 1214 no CTCATTGACCTT GTTCTC CAGTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 185 CCTCCTAAGCCCCAG TCTCTCCTTCCCCG 1030 1214 no TCATTGACCT GTTCTC CAGTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 185 CCTCCTAAGCCCCAG TCTCTCCTTCCCCG 1030 1214 no TCTCATTGACCT GTTCTC CAGTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 185 CCTCCTAAGCCCCAG TCTCTCCTTCCCCG 1030 1214 no CTCATTGACCT GTTCTC CAGTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 197 CCTCCTAAGCCCCAG GCTGCGGGAGGG 1030 1226 no TCATTGACCTTC GTTCTC TCTCTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 197 CCTCCTAAGCCCCAG GCTGCGGGAGGG 1030 1226 no TCATTGACCTT GTTCTC TCTCTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 197 CCTCCTAAGCCCCAG GCTGCGGGAGGG 1030 1226 no CTCATTGACCTT GTTCTC TCTCTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 197 CCTCCTAAGCCCCAG GCTGCGGGAGGG 1030 1226 no TCATTGACCT GTTCTC TCTCTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 197 CCTCCTAAGCCCCAG GCTGCGGGAGGG 1030 1226 no TCTCATTGACCT GTTCTC TCTCTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 197 CCTCCTAAGCCCCAG GCTGCGGGAGGG 1030 1226 no CTCATTGACCT GTTCTC TCTCTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 90 TCCTAAGCCCCAGGT GAGGAAGGTTGT 1032 1121 no TCATTGACCTTC TCTCC GCTCCGTAC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 90 TCCTAAGCCCCAGGT GAGGAAGGTTGT 1032 1121 no TCATTGACCTT TCTCC GCTCCGTAC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 90 TCCTAAGCCCCAGGT GAGGAAGGTTGT 1032 1121 no CTCATTGACCTT TCTCC GCTCCGTAC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 90 TCCTAAGCCCCAGGT GAGGAAGGTTGT 1032 1121 no TCATTGACCT TCTCC GCTCCGTAC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 90 TCCTAAGCCCCAGGT GAGGAAGGTTGT 1032 1121 no TCTCATTGACCT TCTCC GCTCCGTAC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 90 TCCTAAGCCCCAGGT GAGGAAGGTTGT 1032 1121 no CTCATTGACCT TCTCC GCTCCGTAC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 95 TCCTAAGCCCCAGGT CAGAGGAGGAAG 1032 1126 no TCATTGACCTTC TCTCC GTTGTGCTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 95 TCCTAAGCCCCAGGT CAGAGGAGGAAG 1032 1126 no TCATTGACCTT TCTCC GTTGTGCTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 95 TCCTAAGCCCCAGGT CAGAGGAGGAAG 1032 1126 no CTCATTGACCTT TCTCC GTTGTGCTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 95 TCCTAAGCCCCAGGT CAGAGGAGGAAG 1032 1126 no TCATTGACCT TCTCC GTTGTGCTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 95 TCCTAAGCCCCAGGT CAGAGGAGGAAG 1032 1126 no TCTCATTGACCT TCTCC GTTGTGCTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 95 TCCTAAGCCCCAGGT CAGAGGAGGAAG 1032 1126 no CTCATTGACCT TCTCC GTTGTGCTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 97 TCCTAAGCCCCAGGT GGCAGAGGAGGA 1032 1128 no TCATTGACCTTC TCTCC AGGTTGTG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 97 TCCTAAGCCCCAGGT GGCAGAGGAGGA 1032 1128 no TCATTGACCTT TCTCC AGGTTGTG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 97 TCCTAAGCCCCAGGT GGCAGAGGAGGA 1032 1128 no CTCATTGACCTT TCTCC AGGTTGTG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 97 TCCTAAGCCCCAGGT GGCAGAGGAGGA 1032 1128 no TCATTGACCT TCTCC AGGTTGTG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 97 TCCTAAGCCCCAGGT GGCAGAGGAGGA 1032 1128 no TCTCATTGACCT TCTCC AGGTTGTG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 97 TCCTAAGCCCCAGGT GGCAGAGGAGGA 1032 1128 no CTCATTGACCT TCTCC AGGTTGTG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 99 TCCTAAGCCCCAGGT CTGGCAGAGGAG 1032 1130 no TCATTGACCTTC TCTCC GAAGGTTG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 99 TCCTAAGCCCCAGGT CTGGCAGAGGAG 1032 1130 no TCATTGACCTT TCTCC GAAGGTTG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 99 TCCTAAGCCCCAGGT CTGGCAGAGGAG 1032 1130 no CTCATTGACCTT TCTCC GAAGGTTG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 99 TCCTAAGCCCCAGGT CTGGCAGAGGAG 1032 1130 no TCATTGACCT TCTCC GAAGGTTG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 99 TCCTAAGCCCCAGGT CTGGCAGAGGAG 1032 1130 no TCTCATTGACCT TCTCC GAAGGTTG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 99 TCCTAAGCCCCAGGT CTGGCAGAGGAG 1032 1130 no CTCATTGACCT TCTCC GAAGGTTG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 112 TCCTAAGCCCCAGGT TTCATTGTTCTCCC 1032 1143 no TCATTGACCTTC TCTCC TGGCAGAG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 112 TCCTAAGCCCCAGGT TTCATTGTTCTCCC 1032 1143 no TCATTGACCTT TCTCC TGGCAGAG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 112 TCCTAAGCCCCAGGT TTCATTGTTCTCCC 1032 1143 no CTCATTGACCTT TCTCC TGGCAGAG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 112 TCCTAAGCCCCAGGT TTCATTGTTCTCCC 1032 1143 no TCATTGACCT TCTCC TGGCAGAG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 112 TCCTAAGCCCCAGGT TTCATTGTTCTCCC 1032 1143 no TCTCATTGACCT TCTCC TGGCAGAG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 112 TCCTAAGCCCCAGGT TTCATTGTTCTCCC 1032 1143 no CTCATTGACCT TCTCC TGGCAGAG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 122 TCCTAAGCCCCAGGT CCGCCTCTTCTTCA 1032 1153 no TCATTGACCTTC TCTCC TTGTTCTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 122 TCCTAAGCCCCAGGT CCGCCTCTTCTTCA 1032 1153 no TCATTGACCTT TCTCC TTGTTCTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 122 TCCTAAGCCCCAGGT CCGCCTCTTCTTCA 1032 1153 no CTCATTGACCTT TCTCC TTGTTCTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 122 TCCTAAGCCCCAGGT CCGCCTCTTCTTCA 1032 1153 no TCATTGACCT TCTCC TTGTTCTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 122 TCCTAAGCCCCAGGT CCGCCTCTTCTTCA 1032 1153 no TCTCATTGACCT TCTCC TTGTTCTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 122 TCCTAAGCCCCAGGT CCGCCTCTTCTTCA 1032 1153 no CTCATTGACCT TCTCC TTGTTCTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 123 TCCTAAGCCCCAGGT GCCGCCTCTTCTTC 1032 1154 no TCATTGACCTTC TCTCC ATTGTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 123 TCCTAAGCCCCAGGT GCCGCCTCTTCTTC 1032 1154 no TCATTGACCTT TCTCC ATTGTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 123 TCCTAAGCCCCAGGT GCCGCCTCTTCTTC 1032 1154 no CTCATTGACCTT TCTCC ATTGTTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 123 TCCTAAGCCCCAGGT GCCGCCTCTTCTTC 1032 1154 no TCATTGACCT TCTCC ATTGTTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 123 TCCTAAGCCCCAGGT GCCGCCTCTTCTTC 1032 1154 no TCTCATTGACCT TCTCC ATTGTTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 123 TCCTAAGCCCCAGGT GCCGCCTCTTCTTC 1032 1154 no CTCATTGACCT TCTCC ATTGTTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 125 TCCTAAGCCCCAGGT TGGCCGCCTCTTCT 1032 1156 no TCATTGACCTTC TCTCC TCATTG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 172 TCCTAAGCCCCAGGT CCGCAGTCGAGAC 1032 1156 no TCATTGACCTTC TCTCC ACCATG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 125 TCCTAAGCCCCAGGT TGGCCGCCTCTTCT 1032 1156 no TCATTGACCTT TCTCC TCATTG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 125 TCCTAAGCCCCAGGT TGGCCGCCTCTTCT 1032 1156 no CTCATTGACCTT TCTCC TCATTG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 125 TCCTAAGCCCCAGGT TGGCCGCCTCTTCT 1032 1156 no TCATTGACCT TCTCC TCATTG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 125 TCCTAAGCCCCAGGT TGGCCGCCTCTTCT 1032 1156 no TCTCATTGACCT TCTCC TCATTG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 125 TCCTAAGCCCCAGGT TGGCCGCCTCTTCT 1032 1156 no CTCATTGACCT TCTCC TCATTG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 127 TCCTAAGCCCCAGGT GGTGGCCGCCTCT 1032 1158 no TCATTGACCTTC TCTCC TCTTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 130 TCCTAAGCCCCAGGT GGTGGTGGCCGCC 1032 1158 no TCATTGACCTTC TCTCC TCTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 127 TCCTAAGCCCCAGGT GGTGGCCGCCTCT 1032 1158 no TCATTGACCTT TCTCC TCTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 130 TCCTAAGCCCCAGGT GGTGGTGGCCGCC 1032 1158 no TCATTGACCTT TCTCC TCTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 127 TCCTAAGCCCCAGGT GGTGGCCGCCTCT 1032 1158 no CTCATTGACCTT TCTCC TCTTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 130 TCCTAAGCCCCAGGT GGTGGTGGCCGCC 1032 1158 no CTCATTGACCTT TCTCC TCTTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 127 TCCTAAGCCCCAGGT GGTGGCCGCCTCT 1032 1158 no TCATTGACCT TCTCC TCTTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 130 TCCTAAGCCCCAGGT GGTGGTGGCCGCC 1032 1158 no TCATTGACCT TCTCC TCTTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 127 TCCTAAGCCCCAGGT GGTGGCCGCCTCT 1032 1158 no TCTCATTGACCT TCTCC TCTTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 130 TCCTAAGCCCCAGGT GGTGGTGGCCGCC 1032 1158 no TCTCATTGACCT TCTCC TCTTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 127 TCCTAAGCCCCAGGT GGTGGCCGCCTCT 1032 1158 no CTCATTGACCT TCTCC TCTTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 130 TCCTAAGCCCCAGGT GGTGGTGGCCGCC 1032 1161 no CTCATTGACCT TCTCC TCTTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 172 TCCTAAGCCCCAGGT CCGCAGTCGAGAC 1032 1203 no TCATTGACCTT TCTCC ACCATG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 172 TCCTAAGCCCCAGGT CCGCAGTCGAGAC 1032 1203 no CTCATTGACCTT TCTCC ACCATG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 172 TCCTAAGCCCCAGGT CCGCAGTCGAGAC 1032 1203 no TCATTGACCT TCTCC ACCATG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 172 TCCTAAGCCCCAGGT CCGCAGTCGAGAC 1032 1203 no TCTCATTGACCT TCTCC ACCATG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 172 TCCTAAGCCCCAGGT CCGCAGTCGAGAC 1032 1203 no CTCATTGACCT TCTCC ACCATG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 175 TCCTAAGCCCCAGGT TCCCCGCAGTCGA 1032 1206 no TCATTGACCTTC TCTCC GACAC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 175 TCCTAAGCCCCAGGT TCCCCGCAGTCGA 1032 1206 no TCATTGACCTT TCTCC GACAC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 175 TCCTAAGCCCCAGGT TCCCCGCAGTCGA 1032 1206 no CTCATTGACCTT TCTCC GACAC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 175 TCCTAAGCCCCAGGT TCCCCGCAGTCGA 1032 1206 no TCATTGACCT TCTCC GACAC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 175 TCCTAAGCCCCAGGT TCCCCGCAGTCGA 1032 1206 no TCTCATTGACCT TCTCC GACAC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 175 TCCTAAGCCCCAGGT TCCCCGCAGTCGA 1032 1206 no CTCATTGACCT TCTCC GACAC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 179 TCCTAAGCCCCAGGT TCCTTCCCCGCAGT 1032 1210 no TCATTGACCTTC TCTCC CGAG XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 179 TCCTAAGCCCCAGGT TCCTTCCCCGCAGT 1032 1210 no TCATTGACCTT TCTCC CGAG XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 179 TCCTAAGCCCCAGGT TCCTTCCCCGCAGT 1032 1210 no CTCATTGACCTT TCTCC CGAG XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 179 TCCTAAGCCCCAGGT TCCTTCCCCGCAGT 1032 1210 no TCATTGACCT TCTCC CGAG XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 179 TCCTAAGCCCCAGGT TCCTTCCCCGCAGT 1032 1210 no TCTCATTGACCT TCTCC CGAG XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 179 TCCTAAGCCCCAGGT TCCTTCCCCGCAGT 1032 1210 no CTCATTGACCT TCTCC CGAG XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 183 TCCTAAGCCCCAGGT TCTCTCCTTCCCCG 1032 1214 no TCATTGACCTTC TCTCC CAGTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 183 TCCTAAGCCCCAGGT TCTCTCCTTCCCCG 1032 1214 no TCATTGACCTT TCTCC CAGTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 183 TCCTAAGCCCCAGGT TCTCTCCTTCCCCG 1032 1214 no CTCATTGACCTT TCTCC CAGTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 183 TCCTAAGCCCCAGGT TCTCTCCTTCCCCG 1032 1214 no TCATTGACCT TCTCC CAGTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 183 TCCTAAGCCCCAGGT TCTCTCCTTCCCCG 1032 1214 no TCTCATTGACCT TCTCC CAGTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 183 TCCTAAGCCCCAGGT TCTCTCCTTCCCCG 1032 1214 no CTCATTGACCT TCTCC CAGTC XMRV gag 84.9 AGCGGCGGACCTC 67.6 60 195 TCCTAAGCCCCAGGT GCTGCGGGAGGG 1032 1226 no TCATTGACCTTC TCTCC TCTCTC XMRV gag 83.5 AGCGGCGGACCTC 67 58.3 195 TCCTAAGCCCCAGGT GCTGCGGGAGGG 1032 1226 no TCATTGACCTT TCTCC TCTCTC XMRV gag 82.7 TAGCGGCGGACCT 66.7 56 195 TCCTAAGCCCCAGGT GCTGCGGGAGGG 1032 1226 no CTCATTGACCTT TCTCC TCTCTC XMRV gag 82.5 AGCGGCGGACCTC 66.6 60.9 195 TCCTAAGCCCCAGGT GCTGCGGGAGGG 1032 1226 no TCATTGACCT TCTCC TCTCTC XMRV gag 82.3 ATAGCGGCGGACC 66.5 56 195 TCCTAAGCCCCAGGT GCTGCGGGAGGG 1032 1226 no TCTCATTGACCT TCTCC TCTCTC XMRV gag 81.6 TAGCGGCGGACCT 66.3 58.3 195 TCCTAAGCCCCAGGT GCTGCGGGAGGG 1032 1226 no CTCATTGACCT TCTCC TCTCTC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 173 CCAGGATCTGAGAG AGGCGAAGAGAG 2919 3091 yes ACCCTTACAACC AAGTCAACAAG GCTGACTG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 176 CCAGGATCTGAGAG CAAAGGCGAAGA 2919 3094 yes ACCCTTACAACC AAGTCAACAAG GAGGCTGAC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 122 CAGGATCTGAGAGA TCCTTTAAATCAAG 2920 3041 yes ACCCTTACAACC AGTCAACAAG CACAGTGTACC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 169 CAGGATCTGAGAGA CGAAGAGAGGCT 2920 3088 yes ACCCTTACAACC AGTCAACAAG GACTGGTG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 183 CAGGATCTGAGAGA TCTCCACTCAAAG 2920 3102 yes ACCCTTACAACC AGTCAACAAG GCGAAGAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 174 AGGATCTGAGAGAA CAAAGGCGAAGA 2921 3094 yes CTTACAACCTCT GTCAACAAGC GAGGCTGAC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 174 AGGATCTGAGAGAA CAAAGGCGAAGA 2921 3094 yes ACCCTTACAACC GTCAACAAGC GAGGCTGAC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 181 AGGATCTGAGAGAA CTCCACTCAAAGG 2921 3101 yes CTTACAACCTCT GTCAACAAGC CGAAGAGAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 181 AGGATCTGAGAGAA CTCCACTCAAAGG 2921 3101 yes ACCCTTACAACC GTCAACAAGC CGAAGAGAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 120 GGATCTGAGAGAAG TCCTTTAAATCAAG 2922 3041 yes CTTACAACCTCT TCAACAAGC CACAGTGTACC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 120 GGATCTGAGAGAAG TCCTTTAAATCAAG 2922 3041 yes ACCCTTACAACC TCAACAAGC CACAGTGTACC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 123 GGATCTGAGAGAAG GCATCCTTTAAATC 2922 3044 yes CTTACAACCTCT TCAACAAGC AAGCACAGTG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 181 GGATCTGAGAGAAG TCTCCACTCAAAG 2922 3102 yes CTTACAACCTCT TCAACAAGC GCGAAGAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 181 GGATCTGAGAGAAG TCTCCACTCAAAG 2922 3102 yes ACCCTTACAACC TCAACAAGC GCGAAGAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 124 GATCTGAGAGAAGT AGGCATCCTTTAA 2923 3046 yes CTTACAACCTCT CAACAAGCG ATCAAGCACAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 128 AAGTCAACAAGCGG TCTCAGGCAGAAA 2933 3060 yes CTTACAACCTCT GTGGAAG AAGGCATCC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 128 AAGTCAACAAGCGG TCTCAGGCAGAAA 2933 3060 yes ACCCTTACAACC GTGGAAG AAGGCATCC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 147 AAGTCAACAAGCGG GCTGACTGGTGGG 2933 3079 yes CTTACAACCTCT GTGGAAG GTGGAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 147 AAGTCAACAAGCGG GCTGACTGGTGGG 2933 3079 yes ACCCTTACAACC GTGGAAG GTGGAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 159 AAGTCAACAAGCGG AGGCGAAGAGAG 2933 3091 yes CTTACAACCTCT GTGGAAG GCTGACTG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 159 AAGTCAACAAGCGG AGGCGAAGAGAG 2933 3091 yes ACCCTTACAACC GTGGAAG GCTGACTG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 162 AAGTCAACAAGCGG CAAAGGCGAAGA 2933 3094 yes CTTACAACCTCT GTGGAAG GAGGCTGAC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 162 AAGTCAACAAGCGG CAAAGGCGAAGA 2933 3094 yes ACCCTTACAACC GTGGAAG GAGGCTGAC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 108 AGTCAACAAGCGGG TCCTTTAAATCAAG 2934 3041 yes CTTACAACCTCT TGGAAG CACAGTGTACC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 108 AGTCAACAAGCGGG TCCTTTAAATCAAG 2934 3041 yes ACCCTTACAACC TGGAAG CACAGTGTACC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 111 AGTCAACAAGCGGG GCATCCTTTAAATC 2934 3044 yes CTTACAACCTCT TGGAAG AAGCACAGTG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 111 AGTCAACAAGCGGG GCATCCTTTAAATC 2934 3044 yes ACCCTTACAACC TGGAAG AAGCACAGTG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 113 AGTCAACAAGCGGG AGGCATCCTTTAA 2934 3046 yes CTTACAACCTCT TGGAAG ATCAAGCACAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 113 AGTCAACAAGCGGG AGGCATCCTTTAA 2934 3046 yes ACCCTTACAACC TGGAAG ATCAAGCACAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 132 AGTCAACAAGCGGG TGGAGTCTCAGGC 2934 3065 yes CTTACAACCTCT TGGAAG AGAAAAAGG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 132 AGTCAACAAGCGGG TGGAGTCTCAGGC 2934 3065 yes ACCCTTACAACC TGGAAG AGAAAAAGG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 140 AGTCAACAAGCGGG TGGTGGGGTGGA 2934 3073 yes CTTACAACCTCT TGGAAG GTCTCAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 140 AGTCAACAAGCGGG TGGTGGGGTGGA 2934 3073 yes ACCCTTACAACC TGGAAG GTCTCAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 142 AGTCAACAAGCGGG ACTGGTGGGGTG 2934 3075 yes CTTACAACCTCT TGGAAG GAGTCTC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 142 AGTCAACAAGCGGG ACTGGTGGGGTG 2934 3075 yes ACCCTTACAACC TGGAAG GAGTCTC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 155 AGTCAACAAGCGGG CGAAGAGAGGCT 2934 3088 yes CTTACAACCTCT TGGAAG GACTGGTG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 155 AGTCAACAAGCGGG CGAAGAGAGGCT 2934 3088 yes ACCCTTACAACC TGGAAG GACTGGTG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 200 AGTCAACAAGCGGG TCAGTTGTCCTGA 2934 3133 yes CTTACAACCTCT TGGAAG GATTCCCATC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 200 AGTCAACAAGCGGG TCAGTTGTCCTGA 2934 3133 yes ACCCTTACAACC TGGAAG GATTCCCATC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 106 TCAACAAGCGGGTG TCCTTTAAATCAAG 2936 3041 yes CTTACAACCTCT GAAGAC CACAGTGTACC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 106 TCAACAAGCGGGTG TCCTTTAAATCAAG 2936 3041 yes ACCCTTACAACC GAAGAC CACAGTGTACC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 109 TCAACAAGCGGGTG GCATCCTTTAAATC 2936 3044 yes CTTACAACCTCT GAAGAC AAGCACAGTG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 109 TCAACAAGCGGGTG GCATCCTTTAAATC 2936 3044 yes ACCCTTACAACC GAAGAC AAGCACAGTG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 111 TCAACAAGCGGGTG AGGCATCCTTTAA 2936 3046 yes CTTACAACCTCT GAAGAC ATCAAGCACAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 111 TCAACAAGCGGGTG AGGCATCCTTTAA 2936 3046 yes ACCCTTACAACC GAAGAC ATCAAGCACAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 125 TCAACAAGCGGGTG TCTCAGGCAGAAA 2936 3060 yes CTTACAACCTCT GAAGAC AAGGCATCC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 125 TCAACAAGCGGGTG TCTCAGGCAGAAA 2936 3060 yes ACCCTTACAACC GAAGAC AAGGCATCC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 130 TCAACAAGCGGGTG TGGAGTCTCAGGC 2936 3065 yes CTTACAACCTCT GAAGAC AGAAAAAGG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 138 TCAACAAGCGGGTG TGGTGGGGTGGA 2936 3073 yes CTTACAACCTCT GAAGAC GTCTCAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 138 TCAACAAGCGGGTG TGGTGGGGTGGA 2936 3073 yes ACCCTTACAACC GAAGAC GTCTCAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 140 TCAACAAGCGGGTG ACTGGTGGGGTG 2936 3075 yes CTTACAACCTCT GAAGAC GAGTCTC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 140 TCAACAAGCGGGTG ACTGGTGGGGTG 2936 3075 yes ACCCTTACAACC GAAGAC GAGTCTC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 144 TCAACAAGCGGGTG GCTGACTGGTGGG 2936 3079 yes CTTACAACCTCT GAAGAC GTGGAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 144 TCAACAAGCGGGTG GCTGACTGGTGGG 2936 3079 yes ACCCTTACAACC GAAGAC GTGGAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 153 TCAACAAGCGGGTG CGAAGAGAGGCT 2936 3088 yes CTTACAACCTCT GAAGAC GACTGGTG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 153 TCAACAAGCGGGTG CGAAGAGAGGCT 2936 3088 yes ACCCTTACAACC GAAGAC GACTGGTG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 156 TCAACAAGCGGGTG AGGCGAAGAGAG 2936 3091 yes CTTACAACCTCT GAAGAC GCTGACTG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 156 TCAACAAGCGGGTG AGGCGAAGAGAG 2936 3091 yes ACCCTTACAACC GAAGAC GCTGACTG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 159 TCAACAAGCGGGTG CAAAGGCGAAGA 2936 3094 yes CTTACAACCTCT GAAGAC GAGGCTGAC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 159 TCAACAAGCGGGTG CAAAGGCGAAGA 2936 3094 yes ACCCTTACAACC GAAGAC GAGGCTGAC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 167 TCAACAAGCGGGTG TCTCCACTCAAAG 2936 3102 yes CTTACAACCTCT GAAGAC GCGAAGAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 167 TCAACAAGCGGGTG TCTCCACTCAAAG 2936 3102 yes ACCCTTACAACC GAAGAC GCGAAGAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 198 TCAACAAGCGGGTG TCAGTTGTCCTGA 2936 3133 yes CTTACAACCTCT GAAGAC GATTCCCATC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 198 TCAACAAGCGGGTG TCAGTTGTCCTGA 2936 3133 yes ACCCTTACAACC GAAGAC GATTCCCATC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 104 AACAAGCGGGTGGA TCCTTTAAATCAAG 2938 3041 yes CTTACAACCTCT AGACATC CACAGTGTACC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 104 AACAAGCGGGTGGA TCCTTTAAATCAAG 2938 3041 yes ACCCTTACAACC AGACATC CACAGTGTACC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 109 AACAAGCGGGTGGA AGGCATCCTTTAA 2938 3046 yes CTTACAACCTCT AGACATC ATCAAGCACAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 109 AACAAGCGGGTGGA AGGCATCCTTTAA 2938 3046 yes ACCCTTACAACC AGACATC ATCAAGCACAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 123 AACAAGCGGGTGGA TCTCAGGCAGAAA 2938 3060 yes CTTACAACCTCT AGACATC AAGGCATCC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 123 AACAAGCGGGTGGA TCTCAGGCAGAAA 2938 3060 yes ACCCTTACAACC AGACATC AAGGCATCC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 128 AACAAGCGGGTGGA TGGAGTCTCAGGC 2938 3065 yes CTTACAACCTCT AGACATC AGAAAAAGG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 142 AACAAGCGGGTGGA GCTGACTGGTGGG 2938 3079 yes CTTACAACCTCT AGACATC GTGGAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 142 AACAAGCGGGTGGA GCTGACTGGTGGG 2938 3079 yes ACCCTTACAACC AGACATC GTGGAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 154 AACAAGCGGGTGGA AGGCGAAGAGAG 2938 3091 yes CTTACAACCTCT AGACATC GCTGACTG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 154 AACAAGCGGGTGGA AGGCGAAGAGAG 2938 3091 yes ACCCTTACAACC AGACATC GCTGACTG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 157 AACAAGCGGGTGGA CAAAGGCGAAGA 2938 3094 yes CTTACAACCTCT AGACATC GAGGCTGAC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 157 AACAAGCGGGTGGA CAAAGGCGAAGA 2938 3094 yes ACCCTTACAACC AGACATC GAGGCTGAC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 184 AACAAGCGGGTGGA AGATTCCCATCTCT 2938 3121 yes CTTACAACCTCT AGACATC GGATCTCTCC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 184 AACAAGCGGGTGGA AGATTCCCATCTCT 2938 3121 yes ACCCTTACAACC AGACATC GGATCTCTCC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 106 ACAAGCGGGTGGAA GCATCCTTTAAATC 2939 3044 yes CTTACAACCTCT GACATC AAGCACAGTG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 106 ACAAGCGGGTGGAA GCATCCTTTAAATC 2939 3044 yes ACCCTTACAACC GACATC AAGCACAGTG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 135 ACAAGCGGGTGGAA TGGTGGGGTGGA 2939 3073 yes CTTACAACCTCT GACATC GTCTCAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 135 ACAAGCGGGTGGAA TGGTGGGGTGGA 2939 3073 yes ACCCTTACAACC GACATC GTCTCAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 137 ACAAGCGGGTGGAA ACTGGTGGGGTG 2939 3075 yes CTTACAACCTCT GACATC GAGTCTC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 137 ACAAGCGGGTGGAA ACTGGTGGGGTG 2939 3075 yes ACCCTTACAACC GACATC GAGTCTC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 150 ACAAGCGGGTGGAA CGAAGAGAGGCT 2939 3088 yes CTTACAACCTCT GACATC GACTGGTG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 150 ACAAGCGGGTGGAA CGAAGAGAGGCT 2939 3088 yes ACCCTTACAACC GACATC GACTGGTG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 164 ACAAGCGGGTGGAA TCTCCACTCAAAG 2939 3102 yes CTTACAACCTCT GACATC GCGAAGAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 164 ACAAGCGGGTGGAA TCTCCACTCAAAG 2939 3102 yes ACCCTTACAACC GACATC GCGAAGAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 195 ACAAGCGGGTGGAA TCAGTTGTCCTGA 2939 3133 yes CTTACAACCTCT GACATC GATTCCCATC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 195 ACAAGCGGGTGGAA TCAGTTGTCCTGA 2939 3133 yes ACCCTTACAACC GACATC GATTCCCATC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 198 ACAAGCGGGTGGAA AGGTCAGTTGTCC 2939 3136 yes CTTACAACCTCT GACATC TGAGATTCC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 198 ACAAGCGGGTGGAA AGGTCAGTTGTCC 2939 3136 yes ACCCTTACAACC GACATC TGAGATTCC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 102 CAAGCGGGTGGAAG TCCTTTAAATCAAG 2940 3041 yes CTTACAACCTCT ACATCC CACAGTGTACC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 102 CAAGCGGGTGGAAG TCCTTTAAATCAAG 2940 3041 yes ACCCTTACAACC ACATCC CACAGTGTACC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 107 CAAGCGGGTGGAAG AGGCATCCTTTAA 2940 3046 yes CTTACAACCTCT ACATCC ATCAAGCACAG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 107 CAAGCGGGTGGAAG AGGCATCCTTTAA 2940 3046 yes ACCCTTACAACC ACATCC ATCAAGCACAG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 152 CAAGCGGGTGGAAG AGGCGAAGAGAG 2940 3091 yes CTTACAACCTCT ACATCC GCTGACTG XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 152 CAAGCGGGTGGAAG AGGCGAAGAGAG 2940 3091 yes ACCCTTACAACC ACATCC GCTGACTG XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 155 CAAGCGGGTGGAAG CAAAGGCGAAGA 2940 3094 yes CTTACAACCTCT ACATCC GAGGCTGAC XMRV pol 75.1 CCCACCGTGCCCA 68.8 64 155 CAAGCGGGTGGAAG CAAAGGCGAAGA 2940 3094 yes ACCCTTACAACC ACATCC GAGGCTGAC XMRV pol 75.6 ACCGTGCCCAACC 67.1 56 148 AAGCGGGTGGAAGA CGAAGAGAGGCT 2941 3088 yes CTTACAACCTCT CATCC GACTGGTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 116 TGATTTAAAGGATGC GTCTGGTCCAGGT 3030 3145 yes CTCTCTTCGCCT CTTTTTCTGC CAGTTGTC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 116 TGATTTAAAGGATGC GTCTGGTCCAGGT 3030 3145 yes CTCTCTTCGCC CTTTTTCTGC CAGTTGTC XMRV pol 76 CCACCAGTCAGCC 67.3 60 116 TGATTTAAAGGATGC GTCTGGTCCAGGT 3030 3145 yes TCTCTTCGCCTT CTTTTTCTGC CAGTTGTC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 116 TGATTTAAAGGATGC GTCTGGTCCAGGT 3030 3145 yes TCTCTTCGCCT CTTTTTCTGC CAGTTGTC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 126 AAGGATGCCTTTTTC TTTGAAACCCTGT 3037 3162 yes CTCTCTTCGCC TGCCTGAG GGGAGTCTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 165 AAGGATGCCTTTTTC GTCTCTGTGCAGT 3037 3201 yes CTCTCTTCGCC TGCCTGAG GCCTCATC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 84 AGGATGCCTTTTTCT AGATTCCCATCTCT 3038 3121 yes CTCTCTTCGCCT GCCTGAG GGATCTCTCC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 84 AGGATGCCTTTTTCT AGATTCCCATCTCT 3038 3121 yes CTCTCTTCGCC GCCTGAG GGATCTCTCC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 96 AGGATGCCTTTTTCT TCAGTTGTCCTGA 3038 3133 yes CTCTCTTCGCCT GCCTGAG GATTCCCATC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 96 AGGATGCCTTTTTCT TCAGTTGTCCTGA 3038 3133 yes CTCTCTTCGCC GCCTGAG GATTCCCATC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 126 AAGGATGCCTTTTTC TTTGAAACCCTGT 3038 3162 yes CTCTCTTCGCCT TGCCTGAG GGGAGTCTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 149 AGGATGCCTTTTTCT CTCATCAAACAGG 3038 3186 yes CTCTCTTCGCCT GCCTGAG GTGGGACTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 149 AGGATGCCTTTTTCT CTCATCAAACAGG 3038 3186 yes CTCTCTTCGCC GCCTGAG GTGGGACTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 149 AGGATGCCTTTTTCT CTCATCAAACAGG 3038 3186 yes TCTCTTCGCCTT GCCTGAG GTGGGACTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 149 AGGATGCCTTTTTCT CTCATCAAACAGG 3038 3186 yes TCTCTTCGCCT GCCTGAG GTGGGACTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 165 AAGGATGCCTTTTTC GTCTCTGTGCAGT 3038 3201 yes CTCTCTTCGCCT TGCCTGAG GCCTCATC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 178 AGGATGCCTTTTTCT CGGAAATCTGCTA 3038 3215 yes CTCTCTTCGCCT GCCTGAG GGTCTCTGTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 178 AGGATGCCTTTTTCT CGGAAATCTGCTA 3038 3215 yes CTCTCTTCGCC GCCTGAG GGTCTCTGTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 178 AGGATGCCTTTTTCT CGGAAATCTGCTA 3038 3215 yes TCTCTTCGCCTT GCCTGAG GGTCTCTGTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 178 AGGATGCCTTTTTCT CGGAAATCTGCTA 3038 3215 yes TCTCTTCGCCT GCCTGAG GGTCTCTGTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 189 AGGATGCCTTTTTCT GGTGCTGGATCCG 3038 3226 yes CTCTCTTCGCCT GCCTGAG GAAATCTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 189 AGGATGCCTTTTTCT GGTGCTGGATCCG 3038 3226 yes CTCTCTTCGCC GCCTGAG GAAATCTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 98 GGATGCCTTTTTCTG AGGTCAGTTGTCC 3039 3136 yes CTCTCTTCGCCT CCTGAG TGAGATTCC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 98 GGATGCCTTTTTCTG AGGTCAGTTGTCC 3039 3136 yes CTCTCTTCGCC CCTGAG TGAGATTCC XMRV pol 76 CCACCAGTCAGCC 67.3 60 98 GGATGCCTTTTTCTG AGGTCAGTTGTCC 3039 3136 yes TCTCTTCGCCTT CCTGAG TGAGATTCC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 98 GGATGCCTTTTTCTG AGGTCAGTTGTCC 3039 3136 yes TCTCTTCGCCT CCTGAG TGAGATTCC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 107 GGATGCCTTTTTCTG GTCTGGTCCAGGT 3039 3145 yes CTCTCTTCGCCT CCTGAG CAGTTGTC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 107 GGATGCCTTTTTCTG GTCTGGTCCAGGT 3039 3145 yes CTCTCTTCGCC CCTGAG CAGTTGTC XMRV pol 76 CCACCAGTCAGCC 67.3 60 107 GGATGCCTTTTTCTG GTCTGGTCCAGGT 3039 3145 yes TCTCTTCGCCTT CCTGAG CAGTTGTC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 107 GGATGCCTTTTTCTG GTCTGGTCCAGGT 3039 3145 yes TCTCTTCGCCT CCTGAG CAGTTGTC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 109 GGATGCCTTTTTCTG GAGTCTGGTCCAG 3039 3147 no CTCTCTTCGCCT CCTGAG GTCAGTTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 109 GGATGCCTTTTTCTG GAGTCTGGTCCAG 3039 3147 no CTCTCTTCGCC CCTGAG GTCAGTTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 109 GGATGCCTTTTTCTG GAGTCTGGTCCAG 3039 3147 no TCTCTTCGCCTT CCTGAG GTCAGTTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 109 GGATGCCTTTTTCTG GAGTCTGGTCCAG 3039 3147 no TCTCTTCGCCT CCTGAG GTCAGTTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 119 GGATGCCTTTTTCTG AACCCTGTGGGAG 3039 3157 yes CTCTCTTCGCCT CCTGAG TCTGGTC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 119 GGATGCCTTTTTCTG AACCCTGTGGGAG 3039 3157 yes CTCTCTTCGCC CCTGAG TCTGGTC XMRV pol 76 CCACCAGTCAGCC 67.3 60 119 GGATGCCTTTTTCTG AACCCTGTGGGAG 3039 3157 yes TCTCTTCGCCTT CCTGAG TCTGGTC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 119 GGATGCCTTTTTCTG AACCCTGTGGGAG 3039 3157 yes TCTCTTCGCCT CCTGAG TCTGGTC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 124 GGATGCCTTTTTCTG TTTGAAACCCTGT 3039 3162 yes CTCTCTTCGCCT CCTGAG GGGAGTCTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 124 GGATGCCTTTTTCTG TTTGAAACCCTGT 3039 3162 yes CTCTCTTCGCC CCTGAG GGGAGTCTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 124 GGATGCCTTTTTCTG TTTGAAACCCTGT 3039 3162 yes TCTCTTCGCCTT CCTGAG GGGAGTCTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 124 GGATGCCTTTTTCTG TTTGAAACCCTGT 3039 3162 yes TCTCTTCGCCT CCTGAG GGGAGTCTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 157 GGATGCCTTTTTCTG GTGCAGTGCCTCA 3039 3195 yes CTCTCTTCGCCT CCTGAG TCAAACAG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 157 GGATGCCTTTTTCTG GTGCAGTGCCTCA 3039 3195 yes CTCTCTTCGCC CCTGAG TCAAACAG XMRV pol 76 CCACCAGTCAGCC 67.3 60 157 GGATGCCTTTTTCTG GTGCAGTGCCTCA 3039 3195 yes TCTCTTCGCCTT CCTGAG TCAAACAG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 157 GGATGCCTTTTTCTG GTGCAGTGCCTCA 3039 3195 yes TCTCTTCGCCT CCTGAG TCAAACAG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 159 GGATGCCTTTTTCTG CTGTGCAGTGCCT 3039 3197 yes CTCTCTTCGCCT CCTGAG CATCAAAC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 159 GGATGCCTTTTTCTG CTGTGCAGTGCCT 3039 3197 yes CTCTCTTCGCC CCTGAG CATCAAAC XMRV pol 76 CCACCAGTCAGCC 67.3 60 159 GGATGCCTTTTTCTG CTGTGCAGTGCCT 3039 3197 yes TCTCTTCGCCTT CCTGAG CATCAAAC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 159 GGATGCCTTTTTCTG CTGTGCAGTGCCT 3039 3197 yes TCTCTTCGCCT CCTGAG CATCAAAC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 163 GGATGCCTTTTTCTG GTCTCTGTGCAGT 3039 3201 yes CTCTCTTCGCCT CCTGAG GCCTCATC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 163 GGATGCCTTTTTCTG GTCTCTGTGCAGT 3039 3201 yes CTCTCTTCGCC CCTGAG GCCTCATC XMRV pol 76 CCACCAGTCAGCC 67.3 60 163 GGATGCCTTTTTCTG GTCTCTGTGCAGT 3039 3201 yes TCTCTTCGCCTT CCTGAG GCCTCATC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 163 GGATGCCTTTTTCTG GTCTCTGTGCAGT 3039 3201 yes TCTCTTCGCCT CCTGAG GCCTCATC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 168 GGATGCCTTTTTCTG GCTAGGTCTCTGT 3039 3206 yes CTCTCTTCGCCT CCTGAG GCAGTGC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 168 GGATGCCTTTTTCTG GCTAGGTCTCTGT 3039 3206 yes CTCTCTTCGCC CCTGAG GCAGTGC XMRV pol 76 CCACCAGTCAGCC 67.3 60 168 GGATGCCTTTTTCTG GCTAGGTCTCTGT 3039 3206 yes TCTCTTCGCCTT CCTGAG GCAGTGC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 168 GGATGCCTTTTTCTG GCTAGGTCTCTGT 3039 3206 yes TCTCTTCGCCT CCTGAG GCAGTGC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 178 GGATGCCTTTTTCTG CCGGAAATCTGCT 3039 3216 yes CTCTCTTCGCCT CCTGAG AGGTCTCTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 178 GGATGCCTTTTTCTG CCGGAAATCTGCT 3039 3216 yes CTCTCTTCGCC CCTGAG AGGTCTCTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 178 GGATGCCTTTTTCTG CCGGAAATCTGCT 3039 3216 yes TCTCTTCGCCTT CCTGAG AGGTCTCTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 178 GGATGCCTTTTTCTG CCGGAAATCTGCT 3039 3216 yes TCTCTTCGCCT CCTGAG AGGTCTCTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 181 GGATGCCTTTTTCTG GATCCGGAAATCT 3039 3219 yes CTCTCTTCGCCT CCTGAG GCTAGGTCTC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 181 GGATGCCTTTTTCTG GATCCGGAAATCT 3039 3219 yes CTCTCTTCGCC CCTGAG GCTAGGTCTC XMRV pol 76 CCACCAGTCAGCC 67.3 60 181 GGATGCCTTTTTCTG GATCCGGAAATCT 3039 3219 yes TCTCTTCGCCTT CCTGAG GCTAGGTCTC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 181 GGATGCCTTTTTCTG GATCCGGAAATCT 3039 3219 yes TCTCTTCGCCT CCTGAG GCTAGGTCTC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 198 GGATGCCTTTTTCTG ATCAAGTCTGGGT 3039 3236 yes CTCTCTTCGCCT CCTGAG GCTGGATC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 198 GGATGCCTTTTTCTG ATCAAGTCTGGGT 3039 3236 yes CTCTCTTCGCC CCTGAG GCTGGATC XMRV pol 76 CCACCAGTCAGCC 67.3 60 198 GGATGCCTTTTTCTG ATCAAGTCTGGGT 3039 3236 yes TCTCTTCGCCTT CCTGAG GCTGGATC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 198 GGATGCCTTTTTCTG ATCAAGTCTGGGT 3039 3236 yes TCTCTTCGCCT CCTGAG GCTGGATC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 82 GATGCCTTTTTCTGC AGATTCCCATCTCT 3040 3121 yes CTCTCTTCGCCT CTGAGAC GGATCTCTCC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 82 GATGCCTTTTTCTGC AGATTCCCATCTCT 3040 3121 no CTCTCTTCGCC CTGAGAC GGATCTCTCC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 94 GATGCCTTTTTCTGC TCAGTTGTCCTGA 3040 3133 yes CTCTCTTCGCCT CTGAGAC GATTCCCATC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 94 GATGCCTTTTTCTGC TCAGTTGTCCTGA 3040 3133 yes CTCTCTTCGCC CTGAGAC GATTCCCATC XMRV pol 76 CCACCAGTCAGCC 67.3 60 94 GATGCCTTTTTCTGC TCAGTTGTCCTGA 3040 3133 yes TCTCTTCGCCTT CTGAGAC GATTCCCATC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 94 GATGCCTTTTTCTGC TCAGTTGTCCTGA 3040 3133 yes TCTCTTCGCCT CTGAGAC GATTCCCATC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 110 GATGCCTTTTTCTGC GGGAGTCTGGTCC 3040 3149 no CTCTCTTCGCCT CTGAGAC AGGTCAG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 110 GATGCCTTTTTCTGC GGGAGTCTGGTCC 3040 3149 no CTCTCTTCGCC CTGAGAC AGGTCAG XMRV pol 76 CCACCAGTCAGCC 67.3 60 110 GATGCCTTTTTCTGC GGGAGTCTGGTCC 3040 3149 no TCTCTTCGCCTT CTGAGAC AGGTCAG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 110 GATGCCTTTTTCTGC GGGAGTCTGGTCC 3040 3149 no TCTCTTCGCCT CTGAGAC AGGTCAG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 126 GATGCCTTTTTCTGC GTTTTTGAAACCCT 3040 3165 yes CTCTCTTCGCCT CTGAGAC GTGGGAGTC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 126 GATGCCTTTTTCTGC GTTTTTGAAACCCT 3040 3165 yes CTCTCTTCGCC CTGAGAC GTGGGAGTC XMRV pol 76 CCACCAGTCAGCC 67.3 60 126 GATGCCTTTTTCTGC GTTTTTGAAACCCT 3040 3165 yes TCTCTTCGCCTT CTGAGAC GTGGGAGTC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 126 GATGCCTTTTTCTGC GTTTTTGAAACCCT 3040 3165 yes TCTCTTCGCCT CTGAGAC GTGGGAGTC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 132 GATGCCTTTTTCTGC GGGACTGTTTTTG 3040 3171 yes CTCTCTTCGCCT CTGAGAC AAACCCTGTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 132 GATGCCTTTTTCTGC GGGACTGTTTTTG 3040 3171 yes CTCTCTTCGCC CTGAGAC AAACCCTGTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 147 GATGCCTTTTTCTGC CTCATCAAACAGG 3040 3186 yes CTCTCTTCGCCT CTGAGAC GTGGGACTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 147 GATGCCTTTTTCTGC CTCATCAAACAGG 3040 3186 yes CTCTCTTCGCC CTGAGAC GTGGGACTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 147 GATGCCTTTTTCTGC CTCATCAAACAGG 3040 3186 yes TCTCTTCGCCTT CTGAGAC GTGGGACTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 147 GATGCCTTTTTCTGC CTCATCAAACAGG 3040 3186 yes TCTCTTCGCCT CTGAGAC GTGGGACTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 181 GATGCCTTTTTCTGC GGATCCGGAAATC 3040 3220 yes CTCTCTTCGCCT CTGAGAC TGCTAGGTC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 181 GATGCCTTTTTCTGC GGATCCGGAAATC 3040 3220 yes CTCTCTTCGCC CTGAGAC TGCTAGGTC XMRV pol 76 CCACCAGTCAGCC 67.3 60 181 GATGCCTTTTTCTGC GGATCCGGAAATC 3040 3220 yes TCTCTTCGCCTT CTGAGAC TGCTAGGTC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 181 GATGCCTTTTTCTGC GGATCCGGAAATC 3040 3220 yes TCTCTTCGCCT CTGAGAC TGCTAGGTC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 183 GATGCCTTTTTCTGC CTGGATCCGGAAA 3040 3222 yes CTCTCTTCGCCT CTGAGAC TCTGCTAGG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 183 GATGCCTTTTTCTGC CTGGATCCGGAAA 3040 3222 yes CTCTCTTCGCC CTGAGAC TCTGCTAGG XMRV pol 76 CCACCAGTCAGCC 67.3 60 183 GATGCCTTTTTCTGC CTGGATCCGGAAA 3040 3222 yes TCTCTTCGCCTT CTGAGAC TCTGCTAGG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 183 GATGCCTTTTTCTGC CTGGATCCGGAAA 3040 3222 yes TCTCTTCGCCT CTGAGAC TCTGCTAGG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 187 GATGCCTTTTTCTGC GGTGCTGGATCCG 3040 3226 yes CTCTCTTCGCCT CTGAGAC GAAATCTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 187 GATGCCTTTTTCTGC GGTGCTGGATCCG 3040 3226 yes CTCTCTTCGCC CTGAGAC GAAATCTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 187 GATGCCTTTTTCTGC GGTGCTGGATCCG 3040 3226 yes TCTCTTCGCCTT CTGAGAC GAAATCTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 187 GATGCCTTTTTCTGC GGTGCTGGATCCG 3040 3226 yes TCTCTTCGCCT CTGAGAC GAAATCTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 188 GATGCCTTTTTCTGC GGGTGCTGGATCC 3040 3227 yes CTCTCTTCGCCT CTGAGAC GGAAATC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 188 GATGCCTTTTTCTGC GGGTGCTGGATCC 3040 3227 yes CTCTCTTCGCC CTGAGAC GGAAATC XMRV pol 76 CCACCAGTCAGCC 67.3 60 188 GATGCCTTTTTCTGC GGGTGCTGGATCC 3040 3227 yes TCTCTTCGCCTT CTGAGAC GGAAATC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 188 GATGCCTTTTTCTGC GGGTGCTGGATCC 3040 3227 yes TCTCTTCGCCT CTGAGAC GGAAATC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 200 GATGCCTTTTTCTGC AGGATCAAGTCTG 3040 3239 yes CTCTCTTCGCCT CTGAGAC GGTGCTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 200 GATGCCTTTTTCTGC AGGATCAAGTCTG 3040 3239 yes CTCTCTTCGCC CTGAGAC GGTGCTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 200 GATGCCTTTTTCTGC AGGATCAAGTCTG 3040 3239 yes TCTCTTCGCCTT CTGAGAC GGTGCTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 200 GATGCCTTTTTCTGC AGGATCAAGTCTG 3040 3239 yes TCTCTTCGCCT CTGAGAC GGTGCTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 96 ATGCCTTTTTCTGCCT AGGTCAGTTGTCC 3041 3136 yes CTCTCTTCGCCT GAGAC TGAGATTCC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 96 ATGCCTTTTTCTGCCT AGGTCAGTTGTCC 3041 3136 yes CTCTCTTCGCC GAGAC TGAGATTCC XMRV pol 76 CCACCAGTCAGCC 67.3 60 96 ATGCCTTTTTCTGCCT AGGTCAGTTGTCC 3041 3136 yes TCTCTTCGCCTT GAGAC TGAGATTCC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 96 ATGCCTTTTTCTGCCT AGGTCAGTTGTCC 3041 3136 yes TCTCTTCGCCT GAGAC TGAGATTCC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 107 ATGCCTTTTTCTGCCT GAGTCTGGTCCAG 3041 3147 no CTCTCTTCGCCT GAGAC GTCAGTTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 107 ATGCCTTTTTCTGCCT GAGTCTGGTCCAG 3041 3147 no CTCTCTTCGCC GAGAC GTCAGTTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 107 ATGCCTTTTTCTGCCT GAGTCTGGTCCAG 3041 3147 no TCTCTTCGCCTT GAGAC GTCAGTTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 107 ATGCCTTTTTCTGCCT GAGTCTGGTCCAG 3041 3147 no TCTCTTCGCCT GAGAC GTCAGTTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 196 ATGCCTTTTTCTGCCT ATCAAGTCTGGGT 3041 3236 yes CTCTCTTCGCCT GAGAC GCTGGATC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 196 ATGCCTTTTTCTGCCT ATCAAGTCTGGGT 3041 3236 yes CTCTCTTCGCC GAGAC GCTGGATC XMRV pol 76 CCACCAGTCAGCC 67.3 60 196 ATGCCTTTTTCTGCCT ATCAAGTCTGGGT 3041 3236 yes TCTCTTCGCCTT GAGAC GCTGGATC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 196 ATGCCTTTTTCTGCCT ATCAAGTCTGGGT 3041 3236 yes TCTCTTCGCCT GAGAC GCTGGATC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 80 TGCCTTTTTCTGCCT AGATTCCCATCTCT 3042 3121 yes CTCTCTTCGCCT GAGACTC GGATCTCTCC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 80 TGCCTTTTTCTGCCT AGATTCCCATCTCT 3042 3121 yes CTCTCTTCGCC GAGACTC GGATCTCTCC XMRV pol 76 CCACCAGTCAGCC 67.3 60 80 TGCCTTTTTCTGCCT AGATTCCCATCTCT 3042 3121 yes TCTCTTCGCCTT GAGACTC GGATCTCTCC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 80 TGCCTTTTTCTGCCT AGATTCCCATCTCT 3042 3121 yes TCTCTTCGCCT GAGACTC GGATCTCTCC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 92 TGCCTTTTTCTGCCT TCAGTTGTCCTGA 3042 3133 yes CTCTCTTCGCCT GAGACTC GATTCCCATC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 92 TGCCTTTTTCTGCCT TCAGTTGTCCTGA 3042 3133 yes CTCTCTTCGCC GAGACTC GATTCCCATC XMRV pol 76 CCACCAGTCAGCC 67.3 60 92 TGCCTTTTTCTGCCT TCAGTTGTCCTGA 3042 3133 yes TCTCTTCGCCTT GAGACTC GATTCCCATC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 92 TGCCTTTTTCTGCCT TCAGTTGTCCTGA 3042 3133 yes TCTCTTCGCCT GAGACTC GATTCCCATC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 104 TGCCTTTTTCTGCCT GTCTGGTCCAGGT 3042 3145 yes CTCTCTTCGCCT GAGACTC CAGTTGTC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 104 TGCCTTTTTCTGCCT GTCTGGTCCAGGT 3042 3145 yes CTCTCTTCGCC GAGACTC CAGTTGTC XMRV pol 76 CCACCAGTCAGCC 67.3 60 104 TGCCTTTTTCTGCCT GTCTGGTCCAGGT 3042 3145 yes TCTCTTCGCCTT GAGACTC CAGTTGTC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 104 TGCCTTTTTCTGCCT GTCTGGTCCAGGT 3042 3145 yes TCTCTTCGCCT GAGACTC CAGTTGTC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 130 TGCCTTTTTCTGCCT GGGACTGTTTTTG 3042 3171 yes CTCTCTTCGCCT GAGACTC AAACCCTGTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 130 TGCCTTTTTCTGCCT GGGACTGTTTTTG 3042 3171 yes CTCTCTTCGCC GAGACTC AAACCCTGTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 130 TGCCTTTTTCTGCCT GGGACTGTTTTTG 3042 3171 yes TCTCTTCGCCTT GAGACTC AAACCCTGTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 130 TGCCTTTTTCTGCCT GGGACTGTTTTTG 3042 3171 yes TCTCTTCGCCT GAGACTC AAACCCTGTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 145 TGCCTTTTTCTGCCT CTCATCAAACAGG 3042 3186 yes CTCTCTTCGCCT GAGACTC GTGGGACTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 145 TGCCTTTTTCTGCCT CTCATCAAACAGG 3042 3186 yes CTCTCTTCGCC GAGACTC GTGGGACTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 145 TGCCTTTTTCTGCCT CTCATCAAACAGG 3042 3186 yes TCTCTTCGCCTT GAGACTC GTGGGACTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 145 TGCCTTTTTCTGCCT CTCATCAAACAGG 3042 3186 yes TCTCTTCGCCT GAGACTC GTGGGACTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 154 TGCCTTTTTCTGCCT GTGCAGTGCCTCA 3042 3195 yes CTCTCTTCGCCT GAGACTC TCAAACAG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 154 TGCCTTTTTCTGCCT GTGCAGTGCCTCA 3042 3195 yes CTCTCTTCGCC GAGACTC TCAAACAG XMRV pol 76 CCACCAGTCAGCC 67.3 60 154 TGCCTTTTTCTGCCT GTGCAGTGCCTCA 3042 3195 yes TCTCTTCGCCTT GAGACTC TCAAACAG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 154 TGCCTTTTTCTGCCT GTGCAGTGCCTCA 3042 3195 yes TCTCTTCGCCT GAGACTC TCAAACAG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 156 TGCCTTTTTCTGCCT CTGTGCAGTGCCT 3042 3197 yes CTCTCTTCGCCT GAGACTC CATCAAAC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 156 TGCCTTTTTCTGCCT CTGTGCAGTGCCT 3042 3197 yes CTCTCTTCGCC GAGACTC CATCAAAC XMRV pol 76 CCACCAGTCAGCC 67.3 60 156 TGCCTTTTTCTGCCT CTGTGCAGTGCCT 3042 3197 yes TCTCTTCGCCTT GAGACTC CATCAAAC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 156 TGCCTTTTTCTGCCT CTGTGCAGTGCCT 3042 3197 yes TCTCTTCGCCT GAGACTC CATCAAAC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 160 TGCCTTTTTCTGCCT GTCTCTGTGCAGT 3042 3201 yes CTCTCTTCGCCT GAGACTC GCCTCATC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 160 TGCCTTTTTCTGCCT GTCTCTGTGCAGT 3042 3201 yes CTCTCTTCGCC GAGACTC GCCTCATC XMRV pol 76 CCACCAGTCAGCC 67.3 60 160 TGCCTTTTTCTGCCT GTCTCTGTGCAGT 3042 3201 yes TCTCTTCGCCTT GAGACTC GCCTCATC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 160 TGCCTTTTTCTGCCT GTCTCTGTGCAGT 3042 3201 yes TCTCTTCGCCT GAGACTC GCCTCATC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 174 TGCCTTTTTCTGCCT CGGAAATCTGCTA 3042 3215 yes CTCTCTTCGCCT GAGACTC GGTCTCTGTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 174 TGCCTTTTTCTGCCT CGGAAATCTGCTA 3042 3215 yes CTCTCTTCGCC GAGACTC GGTCTCTGTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 174 TGCCTTTTTCTGCCT CGGAAATCTGCTA 3042 3215 yes TCTCTTCGCCTT GAGACTC GGTCTCTGTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 174 TGCCTTTTTCTGCCT CGGAAATCTGCTA 3042 3215 yes TCTCTTCGCCT GAGACTC GGTCTCTGTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 175 TGCCTTTTTCTGCCT CCGGAAATCTGCT 3042 3216 yes CTCTCTTCGCCT GAGACTC AGGTCTCTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 175 TGCCTTTTTCTGCCT CCGGAAATCTGCT 3042 3216 yes CTCTCTTCGCC GAGACTC AGGTCTCTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 175 TGCCTTTTTCTGCCT CCGGAAATCTGCT 3042 3216 yes TCTCTTCGCCTT GAGACTC AGGTCTCTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 175 TGCCTTTTTCTGCCT CCGGAAATCTGCT 3042 3216 yes TCTCTTCGCCT GAGACTC AGGTCTCTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 179 TGCCTTTTTCTGCCT GGATCCGGAAATC 3042 3220 yes CTCTCTTCGCCT GAGACTC TGCTAGGTC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 179 TGCCTTTTTCTGCCT GGATCCGGAAATC 3042 3220 yes CTCTCTTCGCC GAGACTC TGCTAGGTC XMRV pol 76 CCACCAGTCAGCC 67.3 60 179 TGCCTTTTTCTGCCT GGATCCGGAAATC 3042 3220 yes TCTCTTCGCCTT GAGACTC TGCTAGGTC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 179 TGCCTTTTTCTGCCT GGATCCGGAAATC 3042 3220 yes TCTCTTCGCCT GAGACTC TGCTAGGTC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 181 TGCCTTTTTCTGCCT CTGGATCCGGAAA 3042 3222 yes CTCTCTTCGCCT GAGACTC TCTGCTAGG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 181 TGCCTTTTTCTGCCT CTGGATCCGGAAA 3042 3222 yes CTCTCTTCGCC GAGACTC TCTGCTAGG XMRV pol 76 CCACCAGTCAGCC 67.3 60 181 TGCCTTTTTCTGCCT CTGGATCCGGAAA 3042 3222 yes TCTCTTCGCCTT GAGACTC TCTGCTAGG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 181 TGCCTTTTTCTGCCT CTGGATCCGGAAA 3042 3222 yes TCTCTTCGCCT GAGACTC TCTGCTAGG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 185 TGCCTTTTTCTGCCT GGTGCTGGATCCG 3042 3226 yes CTCTCTTCGCCT GAGACTC GAAATCTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 185 TGCCTTTTTCTGCCT GGTGCTGGATCCG 3042 3226 yes CTCTCTTCGCC GAGACTC GAAATCTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 185 TGCCTTTTTCTGCCT GGTGCTGGATCCG 3042 3226 yes TCTCTTCGCCTT GAGACTC GAAATCTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 185 TGCCTTTTTCTGCCT GGTGCTGGATCCG 3042 3226 yes TCTCTTCGCCT GAGACTC GAAATCTG XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 186 TGCCTTTTTCTGCCT GGGTGCTGGATCC 3042 3227 yes CTCTCTTCGCCT GAGACTC GGAAATC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 186 TGCCTTTTTCTGCCT GGGTGCTGGATCC 3042 3227 yes CTCTCTTCGCC GAGACTC GGAAATC XMRV pol 76 CCACCAGTCAGCC 67.3 60 186 TGCCTTTTTCTGCCT GGGTGCTGGATCC 3042 3227 yes TCTCTTCGCCTT GAGACTC GGAAATC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 186 TGCCTTTTTCTGCCT GGGTGCTGGATCC 3042 3227 yes TCTCTTCGCCT GAGACTC GGAAATC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 94 GCCTTTTTCTGCCTG AGGTCAGTTGTCC 3043 3136 yes CTCTCTTCGCCT AGACTC TGAGATTCC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 94 GCCTTTTTCTGCCTG AGGTCAGTTGTCC 3043 3136 yes CTCTCTTCGCC AGACTC TGAGATTCC XMRV pol 76 CCACCAGTCAGCC 67.3 60 94 GCCTTTTTCTGCCTG AGGTCAGTTGTCC 3043 3136 yes TCTCTTCGCCTT AGACTC TGAGATTCC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 94 GCCTTTTTCTGCCTG AGGTCAGTTGTCC 3043 3136 yes TCTCTTCGCCT AGACTC TGAGATTCC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 194 GCCTTTTTCTGCCTG ATCAAGTCTGGGT 3043 3236 yes CTCTCTTCGCCT AGACTC GCTGGATC XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 194 GCCTTTTTCTGCCTG ATCAAGTCTGGGT 3043 3236 yes CTCTCTTCGCC AGACTC GCTGGATC XMRV pol 76 CCACCAGTCAGCC 67.3 60 194 GCCTTTTTCTGCCTG ATCAAGTCTGGGT 3043 3236 yes TCTCTTCGCCTT AGACTC GCTGGATC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 194 GCCTTTTTCTGCCTG ATCAAGTCTGGGT 3043 3236 yes TCTCTTCGCCT AGACTC GCTGGATC XMRV pol 77.2 CCCACCAGTCAGC 68.9 64 197 GCCTTTTTCTGCCTG AGGATCAAGTCTG 3043 3239 yes CTCTCTTCGCCT AGACTC GGTGCTG XMRV pol 76.5 CCCACCAGTCAGC 67.7 66.7 197 GCCTTTTTCTGCCTG AGGATCAAGTCTG 3043 3239 yes CTCTCTTCGCC AGACTC GGTGCTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 89 CTTTTTCTGCCTGAG TCAGTTGTCCTGA 3045 3133 yes TCTCTTCGCCTT ACTCCAC GATTCCCATC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 89 CTTTTTCTGCCTGAG TCAGTTGTCCTGA 3045 3133 yes TCTCTTCGCCT ACTCCAC GATTCCCATC XMRV pol 76 CCACCAGTCAGCC 67.3 60 92 CTTTTTCTGCCTGAG AGGTCAGTTGTCC 3045 3136 yes TCTCTTCGCCTT ACTCCAC TGAGATTCC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 92 CTTTTTCTGCCTGAG AGGTCAGTTGTCC 3045 3136 yes TCTCTTCGCCT ACTCCAC TGAGATTCC XMRV pol 76 CCACCAGTCAGCC 67.3 60 101 CTTTTTCTGCCTGAG GTCTGGTCCAGGT 3045 3145 yes TCTCTTCGCCTT ACTCCAC CAGTTGTC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 101 CTTTTTCTGCCTGAG GTCTGGTCCAGGT 3045 3145 yes TCTCTTCGCCT ACTCCAC CAGTTGTC XMRV pol 76 CCACCAGTCAGCC 67.3 60 151 CTTTTTCTGCCTGAG GTGCAGTGCCTCA 3045 3195 yes TCTCTTCGCCTT ACTCCAC TCAAACAG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 151 CTTTTTCTGCCTGAG GTGCAGTGCCTCA 3045 3195 yes TCTCTTCGCCT ACTCCAC TCAAACAG XMRV pol 76 CCACCAGTCAGCC 67.3 60 153 CTTTTTCTGCCTGAG CTGTGCAGTGCCT 3045 3197 yes TCTCTTCGCCTT ACTCCAC CATCAAAC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 153 CTTTTTCTGCCTGAG CTGTGCAGTGCCT 3045 3197 yes TCTCTTCGCCT ACTCCAC CATCAAAC XMRV pol 76 CCACCAGTCAGCC 67.3 60 158 CCTTTTTCTGCCTGA GTCTCTGTGCAGT 3045 3201 yes TCTCTTCGCCTT GACTCCAC GCCTCATC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 158 CCTTTTTCTGCCTGA GTCTCTGTGCAGT 3045 3201 yes TCTCTTCGCCT GACTCCAC GCCTCATC XMRV pol 76 CCACCAGTCAGCC 67.3 60 172 CCTTTTTCTGCCTGA CGGAAATCTGCTA 3045 3215 yes TCTCTTCGCCTT GACTCCAC GGTCTCTGTG XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 172 CCTTTTTCTGCCTGA CGGAAATCTGCTA 3045 3215 yes TCTCTTCGCCT GACTCCAC GGTCTCTGTG XMRV pol 76 CCACCAGTCAGCC 67.3 60 192 CTTTTTCTGCCTGAG ATCAAGTCTGGGT 3045 3236 yes TCTCTTCGCCTT ACTCCAC GCTGGATC XMRV pol 75.5 CCACCAGTCAGCC 67 62.5 192 CTTTTTCTGCCTGAG ATCAAGTCTGGGT 3045 3236 yes TCTCTTCGCCT ACTCCAC GCTGGATC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 94 AAACATGGGGACTA ACGCGGGGCCCTA 6367 6460 no CTGACCCGCCA AGACTGTATCG CATTG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 135 AACATGGGGACTAA GGGGGTAGCTGTT 6368 6502 no CTGACCCGCCA GACTGTATCG CAGTGATC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 172 AACATGGGGACTAA AGGAGTCCTGGG 6368 6539 no CTGACCCGCCA GACTGTATCG GAGCATG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 200 AACATGGGGACTAA TAGAGGCCGCGCC 6368 6567 no CTGACCCGCCA GACTGTATCG TGAAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 90 ACATGGGGACTAAG GCGGGGCCCTACA 6369 6458 no CTGACCCGCCA ACTGTATCG TTGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 115 ACATGGGGACTAAG TCACGGGATTAGG 6369 6483 no CTGACCCGCCA ACTGTATCG CCCAATG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 122 ACATGGGGACTAAG TCAGTGATCACGG 6369 6490 no CTGACCCGCCA ACTGTATCG GATTAGGC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 126 ACATGGGGACTAAG CTGTTCAGTGATC 6369 6494 no CTGACCCGCCA ACTGTATCG ACGGGATTAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 155 ACATGGGGACTAAG ATGATCTGCACGG 6369 6523 no CTGACCCGCCA ACTGTATCG GTTGGG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 159 AACATGGGGACTAA AGCATGATCTGCA 6369 6526 no CTGACCCGCCA GACTGTATCG CGGGTTG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 167 ACATGGGGACTAAG GTCCTGGGGAGCA 6369 6535 no CTGACCCGCCA ACTGTATCG TGATCTG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 169 ACATGGGGACTAAG GAGTCCTGGGGA 6369 6537 no CTGACCCGCCA ACTGTATCG GCATGATC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 189 ACATGGGGACTAAG GCCTGAAGGAGG 6369 6557 no CTGACCCGCCA ACTGTATCG AGGACGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 195 AAACATGGGGACTA CCGCGCCTGAAGG 6369 6561 no CTGACCCGCCA AGACTGTATCG AGGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 193 ACATGGGGACTAAG CCGCGCCTGAAGG 6369 6561 no CTGACCCGCCA ACTGTATCG AGGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 189 CATGGGGACTAAGA CGCCTGAAGGAG 6370 6558 no CTGACCCGCCA CTGTATCG GAGGAC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 153 ATGGGGACTAAGAC ATGATCTGCACGG 6371 6523 no CTGACCCGCCA TGTATCGATC GTTGGG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 182 ATGGGGACTAAGAC AAGGAGGAGGAC 6371 6552 no CTGACCCGCCA TGTATCGATC GAGGAGTC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 180 GGGGACTAAGACTG AAGGAGGAGGAC 6373 6552 no CTGACCCGCCA TATCGATCC GAGGAGTC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 86 GGACTAAGACTGTA ACGCGGGGCCCTA 6375 6460 no CTGACCCGCCA TCGATCCACTG CATTG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 109 GGACTAAGACTGTA TCACGGGATTAGG 6375 6483 no CTGACCCGCCA TCGATCCACTG CCCAATG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 149 GGACTAAGACTGTA ATGATCTGCACGG 6375 6523 no CTGACCCGCCA TCGATCCACTG GTTGGG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 152 GGACTAAGACTGTA AGCATGATCTGCA 6375 6526 no CTGACCCGCCA TCGATCCACTG CGGGTTG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 178 GGACTAAGACTGTA AAGGAGGAGGAC 6375 6552 no CTGACCCGCCA TCGATCCACTG GAGGAGTC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 187 GGACTAAGACTGTA CCGCGCCTGAAGG 6375 6561 no CTGACCCGCCA TCGATCCACTG AGGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 193 GGACTAAGACTGTA TAGAGGCCGCGCC 6375 6567 no CTGACCCGCCA TCGATCCACTG TGAAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 83 GACTAAGACTGTATC GCGGGGCCCTACA 6376 6458 no CTGACCCGCCA GATCCACTG TTGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 108 GACTAAGACTGTATC TCACGGGATTAGG 6376 6483 no CTGACCCGCCA GATCCACTG CCCAATG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 148 GACTAAGACTGTATC ATGATCTGCACGG 6376 6523 no CTGACCCGCCA GATCCACTG GTTGGG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 162 GACTAAGACTGTATC GAGTCCTGGGGA 6376 6537 no CTGACCCGCCA GATCCACTG GCATGATC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 183 GACTAAGACTGTATC CGCCTGAAGGAG 6376 6558 no CTGACCCGCCA GATCCACTG GAGGAC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 150 ACTAAGACTGTATCG AGCATGATCTGCA 6377 6526 no CTGACCCGCCA ATCCACTGG CGGGTTG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 159 ACTAAGACTGTATCG GTCCTGGGGAGCA 6377 6535 no CTGACCCGCCA ATCCACTGG TGATCTG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 163 ACTAAGACTGTATCG AGGAGTCCTGGG 6377 6539 no CTGACCCGCCA ATCCACTGG GAGCATG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 176 ACTAAGACTGTATCG AAGGAGGAGGAC 6377 6552 no CTGACCCGCCA ATCCACTGG GAGGAGTC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 185 ACTAAGACTGTATCG CCGCGCCTGAAGG 6377 6561 no CTGACCCGCCA ATCCACTGG AGGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 191 ACTAAGACTGTATCG TAGAGGCCGCGCC 6377 6567 no CTGACCCGCCA ATCCACTGG TGAAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 106 CTAAGACTGTATCGA TCACGGGATTAGG 6378 6483 no CTGACCCGCCA TCCACTGG CCCAATG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 146 CTAAGACTGTATCGA ATGATCTGCACGG 6378 6523 no CTGACCCGCCA TCCACTGG GTTGGG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 160 CTAAGACTGTATCGA GAGTCCTGGGGA 6378 6537 no CTGACCCGCCA TCCACTGG GCATGATC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 181 CTAAGACTGTATCGA CGCCTGAAGGAG 6378 6558 no CTGACCCGCCA TCCACTGG GAGGAC XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 186 ACATGGGGACTAAG TGAAGGAGGAGG 6535 6554 no CTGACCCGCCA ACTGTATCG ACGAGGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 178 ACTAAGACTGTATCG TGAAGGAGGAGG 6535 6554 no CTGACCCGCCA ATCCACTGG ACGAGGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 180 GGACTAAGACTGTA TGAAGGAGGAGG 6535 6554 no CTGACCCGCCA TCGATCCACTG ACGAGGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 184 ATGGGGACTAAGAC TGAAGGAGGAGG 6535 6554 no CTGACCCGCCA TGTATCGATC ACGAGGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 182 GGGGACTAAGACTG TGAAGGAGGAGG 6535 6554 no CTGACCCGCCA TATCGATCC ACGAGGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 191 AAACATGGGGACTA GCCTGAAGGAGG 6538 6557 no CTGACCCGCCA AGACTGTATCG AGGACGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 183 GGACTAAGACTGTA GCCTGAAGGAGG 6538 6557 no CTGACCCGCCA TCGATCCACTG AGGACGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 184 ACATGGGGACTAAG GCCTGAAGGAGG 6538 6557 no CTGACCCGCCA ACTGTATCG AGGACGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 181 ACTAAGACTGTATCG GCCTGAAGGAGG 6538 6557 no CTGACCCGCCA ATCCACTGG AGGACGAG XRMV env 76.9 TGACCCTGTTCTCT 68.1 60 186 TGGGGACTAAGACT GCCTGAAGGAGG 6538 6557 no CTGACCCGCCA GTATCGATCC AGGACGAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 95 CTTCAGGCGCGGCCT GTAGGCTCCTTCT 6550 6644 no ACCTGGGACGGG CTATG ACCAGGTTTAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 111 CTTCAGGCGCGGCCT TGAGGTTGAGGGC 6550 6660 no ACCTGGGACGGG CTATG TAGGTAGG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 116 CTTCAGGCGCGGCCT ACTGGTGAGGTTG 6550 6665 no ACCTGGGACGGG CTATG AGGGCTAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 121 CTTCAGGCGCGGCCT TCGGGACTGGTGA 6550 6670 no ACCTGGGACGGG CTATG GGTTGAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 123 CTTCAGGCGCGGCCT TGTCGGGACTGGT 6550 6672 no ACCTGGGACGGG CTATG GAGGTTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 128 CTTCAGGCGCGGCCT GGTTTTGTCGGGA 6550 6677 no ACCTGGGACGGG CTATG CTGGTGAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 129 CTTCAGGCGCGGCCT GGGTTTTGTCGGG 6550 6678 no ACCTGGGACGGG CTATG ACTGGTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 133 CTTCAGGCGCGGCCT TCTTGGGTTTTGTC 6550 6682 no ACCTGGGACGGG CTATG GGGACTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 142 CTTCAGGCGCGGCCT AGCCAGCACTCTT 6550 6691 no ACCTGGGACGGG CTATG GGGTTTTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 150 CTTCAGGCGCGGCCT CTAGACACAGCCA 6550 6699 no ACCTGGGACGGG CTATG GCACTCTTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 154 CTTCAGGCGCGGCCT GATACTAGACACA 6550 6703 no ACCTGGGACGGG CTATG GCCAGCACTC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 155 CTTCAGGCGCGGCCT CGATACTAGACAC 6550 6704 no ACCTGGGACGGG CTATG AGCCAGCAC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 89 TCAGGCGCGGCCTCT GCTCCTTCTACCAG 6552 6640 no ACCTGGGACGGG ATG GTTTAGCAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 93 TCAGGCGCGGCCTCT GTAGGCTCCTTCT 6552 6644 no ACCTGGGACGGG ATG ACCAGGTTTAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 100 TCAGGCGCGGCCTCT GGGCTAGGTAGG 6552 6651 no ACCTGGGACGGG ATG CTCCTTCTAC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 97 GGCGCGGCCTCTAT GGGCTAGGTAGG 6552 6651 no ACCTGGGACGGG GGTG CTCCTTCTAC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 101 TCAGGCGCGGCCTCT AGGGCTAGGTAG 6552 6652 no ACCTGGGACGGG ATG GCTCCTTC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 109 TCAGGCGCGGCCTCT TGAGGTTGAGGGC 6552 6660 no ACCTGGGACGGG ATG TAGGTAGG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 114 TCAGGCGCGGCCTCT ACTGGTGAGGTTG 6552 6665 no ACCTGGGACGGG ATG AGGGCTAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 138 TCAGGCGCGGCCTCT CCAGCACTCTTGG 6552 6669 no ACCTGGGACGGG ATG GTTTTGTC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 119 TCAGGCGCGGCCTCT TCGGGACTGGTGA 6552 6670 no ACCTGGGACGGG ATG GGTTGAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 121 TCAGGCGCGGCCTCT TGTCGGGACTGGT 6552 6672 no ACCTGGGACGGG ATG GAGGTTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 126 TCAGGCGCGGCCTCT GGTTTTGTCGGGA 6552 6677 no ACCTGGGACGGG ATG CTGGTGAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 127 TCAGGCGCGGCCTCT GGGTTTTGTCGGG 6552 6678 no ACCTGGGACGGG ATG ACTGGTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 131 TCAGGCGCGGCCTCT TCTTGGGTTTTGTC 6552 6682 no ACCTGGGACGGG ATG GGGACTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 140 TCAGGCGCGGCCTCT AGCCAGCACTCTT 6552 6691 no ACCTGGGACGGG ATG GGGTTTTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 143 TCAGGCGCGGCCTCT CACAGCCAGCACT 6552 6694 no ACCTGGGACGGG ATG CTTGGG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 148 TCAGGCGCGGCCTCT CTAGACACAGCCA 6552 6699 no ACCTGGGACGGG ATG GCACTCTTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 152 TCAGGCGCGGCCTCT GATACTAGACACA 6552 6703 no ACCTGGGACGGG ATG GCCAGCACTC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 153 TCAGGCGCGGCCTCT CGATACTAGACAC 6552 6704 no ACCTGGGACGGG ATG AGCCAGCAC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 159 TCAGGCGCGGCCTCT GGGTCCCGATACT 6552 6710 no ACCTGGGACGGG ATG AGACACAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 161 TCAGGCGCGGCCTCT GGGGGTCCCGATA 6552 6712 no ACCTGGGACGGG ATG CTAGACAC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 182 TTCAGGCGCGGCCTC CGGCCACCCCTTC 6552 6732 no ACCTGGGACGGG TATG GTAGTAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 187 TCAGGCGCGGCCTCT CTAGGACGGCCAC 6552 6738 no ACCTGGGACGGG ATG CCCTTC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 180 CAGGCGCGGCCTCT CGGCCACCCCTTC 6553 6732 no ACCTGGGACGGG ATGG GTAGTAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 86 GGCGCGGCCTCTAT GCTCCTTCTACCAG 6555 6640 no ACCTGGGACGGG GGTG GTTTAGCAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 90 GGCGCGGCCTCTAT GTAGGCTCCTTCT 6555 6644 no ACCTGGGACGGG GGTG ACCAGGTTTAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 106 GGCGCGGCCTCTAT TGAGGTTGAGGGC 6555 6660 no ACCTGGGACGGG GGTG TAGGTAGG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 111 GGCGCGGCCTCTAT ACTGGTGAGGTTG 6555 6665 no ACCTGGGACGGG GGTG AGGGCTAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 135 GGCGCGGCCTCTAT CCAGCACTCTTGG 6555 6669 no ACCTGGGACGGG GGTG GTTTTGTC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 116 GGCGCGGCCTCTAT TCGGGACTGGTGA 6555 6670 no ACCTGGGACGGG GGTG GGTTGAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 118 GGCGCGGCCTCTAT TGTCGGGACTGGT 6555 6672 no ACCTGGGACGGG GGTG GAGGTTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 123 GGCGCGGCCTCTAT GGTTTTGTCGGGA 6555 6677 no ACCTGGGACGGG GGTG CTGGTGAG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 124 GGCGCGGCCTCTAT GGGTTTTGTCGGG 6555 6678 no ACCTGGGACGGG GGTG ACTGGTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 128 GGCGCGGCCTCTAT TCTTGGGTTTTGTC 6555 6682 no ACCTGGGACGGG GGTG GGGACTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 137 GGCGCGGCCTCTAT AGCCAGCACTCTT 6555 6691 no ACCTGGGACGGG GGTG GGGTTTTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 140 GGCGCGGCCTCTAT CACAGCCAGCACT 6555 6694 no ACCTGGGACGGG GGTG CTTGGG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 145 GGCGCGGCCTCTAT CTAGACACAGCCA 6555 6699 no ACCTGGGACGGG GGTG GCACTCTTG XRMV env 77.1 CGCCTTCTCAACA 68.5 64 149 GGCGCGGCCTCTAT GATACTAGACACA 6555 6703 no ACCTGGGACGGG GGTG GCCAGCACTC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 150 GGCGCGGCCTCTAT CGATACTAGACAC 6555 6704 no ACCTGGGACGGG GGTG AGCCAGCAC XRMV env 77.1 CGCCTTCTCAACA 68.5 64 178 GGCGCGGCCTCTAT CGGCCACCCCTTC 6555 6732 no ACCTGGGACGGG GGTG GTAGTAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 159 GACGGGAGACAGGC GCAGAGGTATGGT 6605 6763 no ACCAGTCCCGA TGCTAAAC TGGAGTAAGTAC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 159 GACGGGAGACAGGC GCAGAGGTATGGT 6605 6763 no ACCAGTCCCGA TGCTAAAC TGGAGTAAGTAC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 127 ACGGGAGACAGGCT CGGCCACCCCTTC 6606 6732 no ACCAGTCCCGA GCTAAAC GTAGTAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 93 CGGGAGACAGGCTG CTAGACACAGCCA 6607 6699 no ACCAGTCCCGA CTAAAC GCACTCTTG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 93 CGGGAGACAGGCTG CTAGACACAGCCA 6607 6699 no ACCAGTCCCGA CTAAAC GCACTCTTG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 97 CGGGAGACAGGCTG GATACTAGACACA 6607 6703 no ACCAGTCCCGA CTAAAC GCCAGCACTC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 97 CGGGAGACAGGCTG GATACTAGACACA 6607 6703 no ACCAGTCCCGA CTAAAC GCCAGCACTC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 127 ACGGGAGACAGGCT CGGCCACCCCTTC 6607 6732 no ACCAGTCCCGA GCTAAAC GTAGTAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 157 CGGGAGACAGGCTG GCAGAGGTATGGT 6607 6763 no ACCAGTCCCGA CTAAAC TGGAGTAAGTAC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 157 CGGGAGACAGGCTG GCAGAGGTATGGT 6607 6763 no ACCAGTCCCGA CTAAAC TGGAGTAAGTAC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 158 CGGGAGACAGGCTG GGCAGAGGTATG 6607 6764 no ACCAGTCCCGA CTAAAC GTTGGAGTAAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 158 CGGGAGACAGGCTG GGCAGAGGTATG 6607 6764 no ACCAGTCCCGA CTAAAC GTTGGAGTAAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 159 CGGGAGACAGGCTG GGGCAGAGGTAT 6607 6765 no ACCAGTCCCGA CTAAAC GGTTGGAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 159 CGGGAGACAGGCTG GGGCAGAGGTAT 6607 6765 no ACCAGTCCCGA CTAAAC GGTTGGAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 161 CGGGAGACAGGCTG CGGGGCAGAGGT 6607 6767 no ACCAGTCCCGA CTAAAC ATGGTTG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 161 CGGGAGACAGGCTG CGGGGCAGAGGT 6607 6767 no ACCAGTCCCGA CTAAAC ATGGTTG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 163 CGGGAGACAGGCTG GCCGGGGCAGAG 6607 6769 no ACCAGTCCCGA CTAAAC GTATGG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 163 CGGGAGACAGGCTG GCCGGGGCAGAG 6607 6769 no ACCAGTCCCGA CTAAAC GTATGG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 185 CGGGAGACAGGCTG TTGGGAGGTCACG 6607 6791 no ACCAGTCCCGA CTAAAC GAGCAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 185 CGGGAGACAGGCTG TTGGGAGGTCACG 6607 6791 no ACCAGTCCCGA CTAAAC GAGCAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 192 CGGGAGACAGGCTG GCTTGTGTTGGGA 6607 6798 no ACCAGTCCCGA CTAAAC GGTCACG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 192 CGGGAGACAGGCTG GCTTGTGTTGGGA 6607 6798 no ACCAGTCCCGA CTAAAC GGTCACG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 196 CGGGAGACAGGCTG GTCAGCTTGTGTT 6607 6802 no ACCAGTCCCGA CTAAAC GGGAGGTC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 196 CGGGAGACAGGCTG GTCAGCTTGTGTT 6607 6802 no ACCAGTCCCGA CTAAAC GGGAGGTC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 200 CGGGAGACAGGCTG CAGGGTCAGCTTG 6607 6806 no ACCAGTCCCGA CTAAAC TGTTGGG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 200 CGGGAGACAGGCTG CAGGGTCAGCTTG 6607 6806 no ACCAGTCCCGA CTAAAC TGTTGGG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 103 GGGAGACAGGCTGC GGGTCCCGATACT 6608 6710 no ACCAGTCCCGA TAAACC AGACACAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 103 GGGAGACAGGCTGC GGGTCCCGATACT 6608 6710 no ACCAGTCCCGA TAAACC AGACACAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 178 GGGAGACAGGCTGC GGTCACGGAGCA 6608 6785 no ACCAGTCCCGA TAAACC GTTAGCC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 178 GGGAGACAGGCTGC GGTCACGGAGCA 6608 6785 no ACCAGTCCCGA TAAACC GTTAGCC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 181 GGGAGACAGGCTGC GGAGGTCACGGA 6608 6788 no ACCAGTCCCGA TAAACC GCAGTTAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 181 GGGAGACAGGCTGC GGAGGTCACGGA 6608 6788 no ACCAGTCCCGA TAAACC GCAGTTAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 152 GACAGGCTGCTAAA GCAGAGGTATGGT 6612 6763 no ACCAGTCCCGA CCTGGTAG TGGAGTAAGTAC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 152 GACAGGCTGCTAAA GCAGAGGTATGGT 6612 6763 no ACCAGTCCCGA CCTGGTAG TGGAGTAAGTAC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 153 GACAGGCTGCTAAA GGCAGAGGTATG 6612 6764 no ACCAGTCCCGA CCTGGTAG GTTGGAGTAAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 153 GACAGGCTGCTAAA GGCAGAGGTATG 6612 6764 no ACCAGTCCCGA CCTGGTAG GTTGGAGTAAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 195 GACAGGCTGCTAAA CAGGGTCAGCTTG 6612 6806 no ACCAGTCCCGA CCTGGTAG TGTTGGG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 195 GACAGGCTGCTAAA CAGGGTCAGCTTG 6612 6806 no ACCAGTCCCGA CCTGGTAG TGTTGGG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 98 ACAGGCTGCTAAAC GGGTCCCGATACT 6613 6710 no ACCAGTCCCGA CTGGTAG AGACACAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 98 ACAGGCTGCTAAAC GGGTCCCGATACT 6613 6710 no ACCAGTCCCGA CTGGTAG AGACACAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 153 ACAGGCTGCTAAAC GGGCAGAGGTAT 6613 6765 no ACCAGTCCCGA CTGGTAG GGTTGGAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 153 ACAGGCTGCTAAAC GGGCAGAGGTAT 6613 6765 no ACCAGTCCCGA CTGGTAG GGTTGGAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 176 ACAGGCTGCTAAAC GGAGGTCACGGA 6613 6788 no ACCAGTCCCGA CTGGTAG GCAGTTAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 176 ACAGGCTGCTAAAC GGAGGTCACGGA 6613 6788 no ACCAGTCCCGA CTGGTAG GCAGTTAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 85 AGGCTGCTAAACCT CTAGACACAGCCA 6615 6699 no ACCAGTCCCGA GGTAGAAG GCACTCTTG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 85 AGGCTGCTAAACCT CTAGACACAGCCA 6615 6699 no ACCAGTCCCGA GGTAGAAG GCACTCTTG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 89 AGGCTGCTAAACCT GATACTAGACACA 6615 6703 no ACCAGTCCCGA GGTAGAAG GCCAGCACTC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 89 AGGCTGCTAAACCT GATACTAGACACA 6615 6703 no ACCAGTCCCGA GGTAGAAG GCCAGCACTC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 96 AGGCTGCTAAACCT GGGTCCCGATACT 6615 6710 no ACCAGTCCCGA GGTAGAAG AGACACAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 96 AGGCTGCTAAACCT GGGTCCCGATACT 6615 6710 no ACCAGTCCCGA GGTAGAAG AGACACAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 150 CAGGCTGCTAAACCT GCAGAGGTATGGT 6615 6763 no ACCAGTCCCGA GGTAGAAG TGGAGTAAGTAC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 150 CAGGCTGCTAAACCT GCAGAGGTATGGT 6615 6763 no ACCAGTCCCGA GGTAGAAG TGGAGTAAGTAC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 150 AGGCTGCTAAACCT GGCAGAGGTATG 6615 6764 no ACCAGTCCCGA GGTAGAAG GTTGGAGTAAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 150 AGGCTGCTAAACCT GGCAGAGGTATG 6615 6764 no ACCAGTCCCGA GGTAGAAG GTTGGAGTAAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 151 AGGCTGCTAAACCT GGGCAGAGGTAT 6615 6765 no ACCAGTCCCGA GGTAGAAG GGTTGGAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 151 AGGCTGCTAAACCT GGGCAGAGGTAT 6615 6765 no ACCAGTCCCGA GGTAGAAG GGTTGGAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 153 AGGCTGCTAAACCT CGGGGCAGAGGT 6615 6767 no ACCAGTCCCGA GGTAGAAG ATGGTTG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 153 AGGCTGCTAAACCT CGGGGCAGAGGT 6615 6767 no ACCAGTCCCGA GGTAGAAG ATGGTTG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 155 AGGCTGCTAAACCT GCCGGGGCAGAG 6615 6769 no ACCAGTCCCGA GGTAGAAG GTATGG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 155 AGGCTGCTAAACCT GCCGGGGCAGAG 6615 6769 no ACCAGTCCCGA GGTAGAAG GTATGG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 171 AGGCTGCTAAACCT GGTCACGGAGCA 6615 6785 no ACCAGTCCCGA GGTAGAAG GTTAGCC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 171 AGGCTGCTAAACCT GGTCACGGAGCA 6615 6785 no ACCAGTCCCGA GGTAGAAG GTTAGCC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 174 AGGCTGCTAAACCT GGAGGTCACGGA 6615 6788 no ACCAGTCCCGA GGTAGAAG GCAGTTAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 174 AGGCTGCTAAACCT GGAGGTCACGGA 6615 6788 no ACCAGTCCCGA GGTAGAAG GCAGTTAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 184 AGGCTGCTAAACCT GCTTGTGTTGGGA 6615 6798 no ACCAGTCCCGA GGTAGAAG GGTCACG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 184 AGGCTGCTAAACCT GCTTGTGTTGGGA 6615 6798 no ACCAGTCCCGA GGTAGAAG GGTCACG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 188 AGGCTGCTAAACCT GTCAGCTTGTGTT 6615 6802 no ACCAGTCCCGA GGTAGAAG GGGAGGTC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 188 AGGCTGCTAAACCT GTCAGCTTGTGTT 6615 6802 no ACCAGTCCCGA GGTAGAAG GGGAGGTC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 192 AGGCTGCTAAACCT CAGGGTCAGCTTG 6615 6806 no ACCAGTCCCGA GGTAGAAG TGTTGGG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 192 AGGCTGCTAAACCT CAGGGTCAGCTTG 6615 6806 no ACCAGTCCCGA GGTAGAAG TGTTGGG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 195 AGGCTGCTAAACCT GGACAGGGTCAG 6615 6809 no ACCAGTCCCGA GGTAGAAG CTTGTGTTG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 195 AGGCTGCTAAACCT GGACAGGGTCAG 6615 6809 no ACCAGTCCCGA GGTAGAAG CTTGTGTTG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 196 AGGCTGCTAAACCT CGGACAGGGTCA 6615 6810 no ACCAGTCCCGA GGTAGAAG GCTTGTG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 196 AGGCTGCTAAACCT CGGACAGGGTCA 6615 6810 no ACCAGTCCCGA GGTAGAAG GCTTGTG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 148 GGCTGCTAAACCTG GCAGAGGTATGGT 6616 6763 no ACCAGTCCCGA GTAGAAGG TGGAGTAAGTAC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 148 GGCTGCTAAACCTG GCAGAGGTATGGT 6616 6763 no ACCAGTCCCGA GTAGAAGG TGGAGTAAGTAC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 83 GCTGCTAAACCTGGT CTAGACACAGCCA 6617 6699 no ACCAGTCCCGA AGAAGGAG GCACTCTTG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 83 GCTGCTAAACCTGGT CTAGACACAGCCA 6617 6699 no ACCAGTCCCGA AGAAGGAG GCACTCTTG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 87 GCTGCTAAACCTGGT GATACTAGACACA 6617 6703 no ACCAGTCCCGA AGAAGGAG GCCAGCACTC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 87 GCTGCTAAACCTGGT GATACTAGACACA 6617 6703 no ACCAGTCCCGA AGAAGGAG GCCAGCACTC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 148 GCTGCTAAACCTGGT GGCAGAGGTATG 6617 6764 no ACCAGTCCCGA AGAAGGAG GTTGGAGTAAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 148 GCTGCTAAACCTGGT GGCAGAGGTATG 6617 6764 no ACCAGTCCCGA AGAAGGAG GTTGGAGTAAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 190 GCTGCTAAACCTGGT CAGGGTCAGCTTG 6617 6806 no ACCAGTCCCGA AGAAGGAG TGTTGGG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 190 GCTGCTAAACCTGGT CAGGGTCAGCTTG 6617 6806 no ACCAGTCCCGA AGAAGGAG TGTTGGG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 193 GCTGCTAAACCTGGT GGACAGGGTCAG 6617 6809 no ACCAGTCCCGA AGAAGGAG CTTGTGTTG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 193 GCTGCTAAACCTGGT GGACAGGGTCAG 6617 6809 no ACCAGTCCCGA AGAAGGAG CTTGTGTTG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 79 CTAAACCTGGTAGA CTAGACACAGCCA 6621 6699 no ACCAGTCCCGA AGGAGCCTAC GCACTCTTG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 79 CTAAACCTGGTAGA CTAGACACAGCCA 6621 6699 no ACCAGTCCCGA AGGAGCCTAC GCACTCTTG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 83 CTAAACCTGGTAGA GATACTAGACACA 6621 6703 no ACCAGTCCCGA AGGAGCCTAC GCCAGCACTC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 83 CTAAACCTGGTAGA GATACTAGACACA 6621 6703 no ACCAGTCCCGA AGGAGCCTAC GCCAGCACTC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 143 CTAAACCTGGTAGA GCAGAGGTATGGT 6621 6763 no ACCAGTCCCGA AGGAGCCTAC TGGAGTAAGTAC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 143 CTAAACCTGGTAGA GCAGAGGTATGGT 6621 6763 no ACCAGTCCCGA AGGAGCCTAC TGGAGTAAGTAC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 144 CTAAACCTGGTAGA GGCAGAGGTATG 6621 6764 no ACCAGTCCCGA AGGAGCCTAC GTTGGAGTAAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 144 CTAAACCTGGTAGA GGCAGAGGTATG 6621 6764 no ACCAGTCCCGA AGGAGCCTAC GTTGGAGTAAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 165 CTAAACCTGGTAGA GGTCACGGAGCA 6621 6785 no ACCAGTCCCGA AGGAGCCTAC GTTAGCC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 165 CTAAACCTGGTAGA GGTCACGGAGCA 6621 6785 no ACCAGTCCCGA AGGAGCCTAC GTTAGCC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 167 TAAACCTGGTAGAA GGAGGTCACGGA 6622 6788 no ACCAGTCCCGA GGAGCCTAC GCAGTTAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 167 TAAACCTGGTAGAA GGAGGTCACGGA 6622 6788 no ACCAGTCCCGA GGAGCCTAC GCAGTTAG XRMV env 76.8 AGCCCTCAACCTC 68 62.5 163 AAACCTGGTAGAAG GGTCACGGAGCA 6623 6785 no ACCAGTCCCGA GAGCCTAC GTTAGCC XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 163 AAACCTGGTAGAAG GGTCACGGAGCA 6623 6785 no ACCAGTCCCGA GAGCCTAC GTTAGCC XRMV env 76.8 AGCCCTCAACCTC 68 62.5 165 AACCTGGTAGAAGG GGAGGTCACGGA 6624 6788 no ACCAGTCCCGA AGCCTAC GCAGTTAG XRMV env 76.5 TAGCCCTCAACCTC 67.7 60 165 AACCTGGTAGAAGG GGAGGTCACGGA 6624 6788 no ACCAGTCCCGA AGCCTAC GCAGTTAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 88 GCATAGGAGCAGTT GCGGGAGAGGCC 6832 6919 no CGAGCGACGG CCCAAAAC AAATAGTAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 88 GCATAGGAGCAGTT GCGGGAGAGGCC 6832 6919 no GACGAGCGACGG CCCAAAAC AAATAGTAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 113 GCATAGGAGCAGTT GGTGCTGCAAGCC 6832 6944 no CGAGCGACGG CCCAAAAC CAAATG XRMV env 75.7 ATACCACCCAGAA 67.1 60 113 GCATAGGAGCAGTT GGTGCTGCAAGCC 6832 6944 no GACGAGCGACGG CCCAAAAC CAAATG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 141 GCATAGGAGCAGTT CAGTAGTAGATAG 6832 6972 no CGAGCGACGG CCCAAAAC ACAGGGAGTGAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 141 GCATAGGAGCAGTT CAGTAGTAGATAG 6832 6972 no GACGAGCGACGG CCCAAAAC ACAGGGAGTGAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 160 GCATAGGAGCAGTT TCAGTGGTTAAGT 6832 6991 no CGAGCGACGG CCCAAAAC TAAGCACAGTAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 160 GCATAGGAGCAGTT TCAGTGGTTAAGT 6832 6991 no GACGAGCGACGG CCCAAAAC TAAGCACAGTAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 173 GCATAGGAGCAGTT CAGGACACAGTAA 6832 7004 no CGAGCGACGG CCCAAAAC TCAGTGGTTAAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 173 GCATAGGAGCAGTT CAGGACACAGTAA 6832 7004 no GACGAGCGACGG CCCAAAAC TCAGTGGTTAAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 178 GCATAGGAGCAGTT TCAACCAGGACAC 6832 7009 no CGAGCGACGG CCCAAAAC AGTAATCAGTG XRMV env 75.7 ATACCACCCAGAA 67.1 60 178 GCATAGGAGCAGTT TCAACCAGGACAC 6832 7009 no GACGAGCGACGG CCCAAAAC AGTAATCAGTG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 180 GCATAGGAGCAGTT GTTCAACCAGGAC 6832 7011 no CGAGCGACGG CCCAAAAC ACAGTAATCAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 180 GCATAGGAGCAGTT GTTCAACCAGGAC 6832 7011 no GACGAGCGACGG CCCAAAAC ACAGTAATCAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 174 GAGCAGTTCCCAAA GTTCAACCAGGAC 6832 7011 no GACGAGCGACGG ACCCATC ACAGTAATCAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 182 GCATAGGAGCAGTT GAGTTCAACCAGG 6832 7013 no CGAGCGACGG CCCAAAAC ACACAGTAATC XRMV env 75.7 ATACCACCCAGAA 67.1 60 182 GCATAGGAGCAGTT GAGTTCAACCAGG 6832 7013 no GACGAGCGACGG CCCAAAAC ACACAGTAATC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 185 GCATAGGAGCAGTT CCAGAGTTCAACC 6832 7016 no CGAGCGACGG CCCAAAAC AGGACACAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 185 GCATAGGAGCAGTT CCAGAGTTCAACC 6832 7016 no GACGAGCGACGG CCCAAAAC AGGACACAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 186 GCATAGGAGCAGTT GCCAGAGTTCAAC 6832 7017 no CGAGCGACGG CCCAAAAC CAGGACAC XRMV env 75.7 ATACCACCCAGAA 67.1 60 186 GCATAGGAGCAGTT GCCAGAGTTCAAC 6832 7017 no GACGAGCGACGG CCCAAAAC CAGGACAC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 187 GCATAGGAGCAGTT GGCCAGAGTTCAA 6832 7018 no CGAGCGACGG CCCAAAAC CCAGGAC XRMV env 75.7 ATACCACCCAGAA 67.1 60 187 GCATAGGAGCAGTT GGCCAGAGTTCAA 6832 7018 no GACGAGCGACGG CCCAAAAC CCAGGAC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 147 CATAGGAGCAGTTC TTAAGCACAGTAG 6833 6979 no CGAGCGACGG CCAAAACC TAGATAGACAGG XRMV env 75.7 ATACCACCCAGAA 67.1 60 147 CATAGGAGCAGTTC TTAAGCACAGTAG 6833 6979 no GACGAGCGACGG CCAAAACC TAGATAGACAGG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 171 ATAGGAGCAGTTCC CAGGACACAGTAA 6834 7004 no CGAGCGACGG CAAAACCC TCAGTGGTTAAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 171 ATAGGAGCAGTTCC CAGGACACAGTAA 6834 7004 no GACGAGCGACGG CAAAACCC TCAGTGGTTAAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 176 ATAGGAGCAGTTCC TCAACCAGGACAC 6834 7009 no CGAGCGACGG CAAAACCC AGTAATCAGTG XRMV env 75.7 ATACCACCCAGAA 67.1 60 176 ATAGGAGCAGTTCC TCAACCAGGACAC 6834 7009 no GACGAGCGACGG CAAAACCC AGTAATCAGTG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 178 ATAGGAGCAGTTCC GTTCAACCAGGAC 6834 7011 no CGAGCGACGG CAAAACCC ACAGTAATCAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 178 ATAGGAGCAGTTCC GTTCAACCAGGAC 6834 7011 no GACGAGCGACGG CAAAACCC ACAGTAATCAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 183 ATAGGAGCAGTTCC CCAGAGTTCAACC 6834 7016 no CGAGCGACGG CAAAACCC AGGACACAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 183 ATAGGAGCAGTTCC CCAGAGTTCAACC 6834 7016 no GACGAGCGACGG CAAAACCC AGGACACAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 184 ATAGGAGCAGTTCC GCCAGAGTTCAAC 6834 7017 no CGAGCGACGG CAAAACCC CAGGACAC XRMV env 75.7 ATACCACCCAGAA 67.1 60 184 ATAGGAGCAGTTCC GCCAGAGTTCAAC 6834 7017 no GACGAGCGACGG CAAAACCC CAGGACAC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 185 ATAGGAGCAGTTCC GGCCAGAGTTCAA 6834 7018 no CGAGCGACGG CAAAACCC CCAGGAC XRMV env 75.7 ATACCACCCAGAA 67.1 60 185 ATAGGAGCAGTTCC GGCCAGAGTTCAA 6834 7018 no GACGAGCGACGG CAAAACCC CCAGGAC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 157 TAGGAGCAGTTCCC TCAGTGGTTAAGT 6835 6991 no CGAGCGACGG AAAACCC TAAGCACAGTAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 157 TAGGAGCAGTTCCC TCAGTGGTTAAGT 6836 6991 no GACGAGCGACGG AAAACCC TAAGCACAGTAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 169 AGGAGCAGTTCCCA CAGGACACAGTAA 6836 7004 no CGAGCGACGG AAACCC TCAGTGGTTAAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 169 AGGAGCAGTTCCCA CAGGACACAGTAA 6836 7004 no GACGAGCGACGG AAACCC TCAGTGGTTAAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 176 AGGAGCAGTTCCCA GTTCAACCAGGAC 6836 7011 no CGAGCGACGG AAACCC ACAGTAATCAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 176 AGGAGCAGTTCCCA GTTCAACCAGGAC 6836 7011 no GACGAGCGACGG AAACCC ACAGTAATCAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 183 AGGAGCAGTTCCCA GGCCAGAGTTCAA 6836 7018 no CGAGCGACGG AAACCC CCAGGAC XRMV env 75.7 ATACCACCCAGAA 67.1 60 183 AGGAGCAGTTCCCA GGCCAGAGTTCAA 6836 7018 no GACGAGCGACGG AAACCC CCAGGAC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 107 GAGCAGTTCCCAAA GGTGCTGCAAGCC 6838 6944 no CGAGCGACGG ACCCATC CAAATG XRMV env 75.7 ATACCACCCAGAA 67.1 60 107 GAGCAGTTCCCAAA GGTGCTGCAAGCC 6838 6944 no GACGAGCGACGG ACCCATC CAAATG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 135 GAGCAGTTCCCAAA CAGTAGTAGATAG 6838 6972 no CGAGCGACGG ACCCATC ACAGGGAGTGAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 135 GAGCAGTTCCCAAA CAGTAGTAGATAG 6838 6972 no GACGAGCGACGG ACCCATC ACAGGGAGTGAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 142 GAGCAGTTCCCAAA TTAAGCACAGTAG 6838 6979 no CGAGCGACGG ACCCATC TAGATAGACAGG XRMV env 75.7 ATACCACCCAGAA 67.1 60 142 GAGCAGTTCCCAAA TTAAGCACAGTAG 6838 6979 no GACGAGCGACGG ACCCATC TAGATAGACAGG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 151 GAGCAGTTCCCAAA GTGGTTAAGTTAA 6838 6988 no CGAGCGACGG ACCCATC GCACAGTAGTAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 151 GAGCAGTTCCCAAA GTGGTTAAGTTAA 6838 6988 no GACGAGCGACGG ACCCATC GCACAGTAGTAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 154 GAGCAGTTCCCAAA TCAGTGGTTAAGT 6838 6991 no CGAGCGACGG ACCCATC TAAGCACAGTAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 154 GAGCAGTTCCCAAA TCAGTGGTTAAGT 6838 6991 no GACGAGCGACGG ACCCATC TAAGCACAGTAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 161 GAGCAGTTCCCAAA ACAGTAATCAGTG 6838 6998 no CGAGCGACGG ACCCATC GTTAAGTTAAGC XRMV env 75.7 ATACCACCCAGAA 67.1 60 161 GAGCAGTTCCCAAA ACAGTAATCAGTG 6838 6998 no GACGAGCGACGG ACCCATC GTTAAGTTAAGC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 167 GAGCAGTTCCCAAA CAGGACACAGTAA 6838 7004 no CGAGCGACGG ACCCATC TCAGTGGTTAAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 167 GAGCAGTTCCCAAA CAGGACACAGTAA 6838 7004 no GACGAGCGACGG ACCCATC TCAGTGGTTAAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 173 GGAGCAGTTCCCAA TCAACCAGGACAC 6838 7009 no CGAGCGACGG AACCCATC AGTAATCAGTG XRMV env 75.7 ATACCACCCAGAA 67.1 60 173 GGAGCAGTTCCCAA TCAACCAGGACAC 6838 7009 no GACGAGCGACGG AACCCATC AGTAATCAGTG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 174 GAGCAGTTCCCAAA GTTCAACCAGGAC 6838 7011 no CGAGCGACGG ACCCATC ACAGTAATCAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 176 GAGCAGTTCCCAAA GAGTTCAACCAGG 6838 7013 no CGAGCGACGG ACCCATC ACACAGTAATC XRMV env 75.7 ATACCACCCAGAA 67.1 60 176 GAGCAGTTCCCAAA GAGTTCAACCAGG 6838 7013 no GACGAGCGACGG ACCCATC ACACAGTAATC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 180 GGAGCAGTTCCCAA CCAGAGTTCAACC 6838 7016 no CGAGCGACGG AACCCATC AGGACACAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 180 GGAGCAGTTCCCAA CCAGAGTTCAACC 6838 7016 no GACGAGCGACGG AACCCATC AGGACACAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 181 GGAGCAGTTCCCAA GCCAGAGTTCAAC 6838 7017 no GACGAGCGACGG AACCCATC CAGGACAC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 181 GAGCAGTTCCCAAA GGCCAGAGTTCAA 6838 7018 no CGAGCGACGG ACCCATC CCAGGAC XRMV env 75.7 ATACCACCCAGAA 67.1 60 181 GAGCAGTTCCCAAA GGCCAGAGTTCAA 6838 7018 no GACGAGCGACGG ACCCATC CCAGGAC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 171 AGCAGTTCCCAAAAC TCAACCAGGACAC 6839 7009 no CGAGCGACGG CCATCAG AGTAATCAGTG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 80 GCAGTTCCCAAAACC GCGGGAGAGGCC 6840 6919 no CGAGCGACGG CATCAG AAATAGTAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 80 GCAGTTCCCAAAACC GCGGGAGAGGCC 6840 6919 no GACGAGCGACGG CATCAG AAATAGTAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 81 GCAGTTCCCAAAACC GGCGGGAGAGGC 6840 6920 no CGAGCGACGG CATCAG CAAATAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 81 GCAGTTCCCAAAACC GGCGGGAGAGGC 6840 6920 no GACGAGCGACGG CATCAG CAAATAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 105 GCAGTTCCCAAAACC GGTGCTGCAAGCC 6840 6944 no CGAGCGACGG CATCAG CAAATG XRMV env 75.7 ATACCACCCAGAA 67.1 60 105 GCAGTTCCCAAAACC GGTGCTGCAAGCC 6840 6944 no GACGAGCGACGG CATCAG CAAATG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 133 GCAGTTCCCAAAACC CAGTAGTAGATAG 6840 6972 no CGAGCGACGG CATCAG ACAGGGAGTGAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 133 GCAGTTCCCAAAACC CAGTAGTAGATAG 6840 6972 no GACGAGCGACGG CATCAG ACAGGGAGTGAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 140 GCAGTTCCCAAAACC TTAAGCACAGTAG 6840 6979 no CGAGCGACGG CATCAG TAGATAGACAGG XRMV env 75.7 ATACCACCCAGAA 67.1 60 140 GCAGTTCCCAAAACC TTAAGCACAGTAG 6840 6979 no GACGAGCGACGG CATCAG TAGATAGACAGG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 149 GCAGTTCCCAAAACC GTGGTTAAGTTAA 6840 6988 no CGAGCGACGG CATCAG GCACAGTAGTAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 149 GCAGTTCCCAAAACC GTGGTTAAGTTAA 6840 6988 no GACGAGCGACGG CATCAG GCACAGTAGTAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 152 GCAGTTCCCAAAACC TCAGTGGTTAAGT 6840 6991 no CGAGCGACGG CATCAG TAAGCACAGTAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 152 GCAGTTCCCAAAACC TCAGTGGTTAAGT 6840 6991 no GACGAGCGACGG CATCAG TAAGCACAGTAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 165 GCAGTTCCCAAAACC CAGGACACAGTAA 6840 7004 no CGAGCGACGG CATCAG TCAGTGGTTAAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 165 GCAGTTCCCAAAACC CAGGACACAGTAA 6840 7004 no GACGAGCGACGG CATCAG TCAGTGGTTAAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 171 AGCAGTTCCCAAAAC TCAACCAGGACAC 6840 7009 no GACGAGCGACGG CCATCAG AGTAATCAGTG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 172 GCAGTTCCCAAAACC GTTCAACCAGGAC 6840 7011 no CGAGCGACGG CATCAG ACAGTAATCAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 172 GCAGTTCCCAAAACC GTTCAACCAGGAC 6840 7011 no GACGAGCGACGG CATCAG ACAGTAATCAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 174 GCAGTTCCCAAAACC GAGTTCAACCAGG 6840 7013 no CGAGCGACGG CATCAG ACACAGTAATC XRMV env 75.7 ATACCACCCAGAA 67.1 60 174 GCAGTTCCCAAAACC GAGTTCAACCAGG 6840 7013 no GACGAGCGACGG CATCAG ACACAGTAATC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 178 AGCAGTTCCCAAAAC CCAGAGTTCAACC 6840 7016 no CGAGCGACGG CCATCAG AGGACACAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 178 AGCAGTTCCCAAAAC CCAGAGTTCAACC 6840 7016 no GACGAGCGACGG CCATCAG AGGACACAG XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 179 AGCAGTTCCCAAAAC GCCAGAGTTCAAC 6840 7017 no CGAGCGACGG CCATCAG CAGGACAC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 181 GGAGCAGTTCCCAA GCCAGAGTTCAAC 6840 7017 no CGAGCGACGG AACCCATC CAGGACAC XRMV env 75.7 ATACCACCCAGAA 67.1 60 179 AGCAGTTCCCAAAAC GCCAGAGTTCAAC 6840 7017 no GACGAGCGACGG CCATCAG CAGGACAC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 179 GCAGTTCCCAAAACC GGCCAGAGTTCAA 6840 7018 no CGAGCGACGG CATCAG CCAGGAC XRMV env 75.7 ATACCACCCAGAA 67.1 60 179 GCAGTTCCCAAAACC GGCCAGAGTTCAA 6840 7018 no GACGAGCGACGG CATCAG CCAGGAC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 158 CAGTTCCCAAAACCC ACAGTAATCAGTG 6841 6998 no CGAGCGACGG ATCAGG GTTAAGTTAAGC XRMV env 75.7 ATACCACCCAGAA 67.1 60 158 CAGTTCCCAAAACCC ACAGTAATCAGTG 6841 6998 no GACGAGCGACGG ATCAGG GTTAAGTTAAGC XRMV env 75.9 ACCACCCAGAAGA 67.2 65.2 176 CAGTTCCCAAAACCC CCAGAGTTCAACC 6841 7016 no CGAGCGACGG ATCAGG AGGACACAG XRMV env 75.7 ATACCACCCAGAA 67.1 60 176 CAGTTCCCAAAACCC CCAGAGTTCAACC 6841 7016 no GACGAGCGACGG ATCAGG AGGACACAG

RT-PCR assay is performed to quantify RNA from biological samples, such as whole blood and plasma, without the need for RNA extraction. The assay employs a two-step amplification process with the initial step consisting of the distribution of 2 μL of experimental sample directly into a cDNA reaction mix. Following completion of the reverse transcriptase (RT) cDNA synthesis, a 2 μL aliquot is removed, transferred into a qPCR reaction mix and a qPCR protocol is performed.

In a separate embodiment, RNA is isolated from cell culture supernatants, whole blood or plasma using QIAamp®viral RNA Mini kit. The RNA is then used for reverse transcription. After reverse transcription, cDNA is subjected to qPCR assay.

A number of embodiments of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims. 

1. An isolated oligonucleotide consisting of a sequence selected from the group consisting of: SEQ ID NO:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, oligonucleotides haying regions of homology between XMRV and MLV and oligonucleotides that are at least 95% identical to any of the foregoing and can hybridize to an MLV-related polynucleotide.
 2. The isolated oligonucleotide of claim 1 comprising a primer pair consisting of SEQ ID NO:1 and 2 and sequence that are at least 95% identical to SEQ ID NO:1 and 2 and hybridize to an MLV-related polynucleotide.
 3. The isolated oligonucleotide of claim 1 comprising a primer pair consisting of SEQ ID NO:4 and 5 and sequence that are at least 95% identical to SEQ ID NO:4 and 5 and hybridize to an MLV-related polynucleotide.
 4. The isolated oligonucleotide of claim 1 comprising a primer pair consisting of SEQ ID NO:7 and 8 and sequence that are at least 95% identical to SEQ ID NO:7 and 8 and hybridize to an MLV-related polynucleotide.
 5. The isolated oligonucleotide of claim 1 comprising a primer pair consisting of SEQ ID NO:10 and 11 and sequence that are at least 95% identical to SEQ ID NO:10 and 11 and hybridize to an MLV-related polynucleotide.
 6. The isolated oligonucleotide of claim 1 comprising a primer pair consisting of SEQ ID NO:13 and 14 and sequence that are at least 95% identical to SEQ ID NO:13 and 14 and hybridize to an MLV-related polynucleotide.
 7. The isolated oligonucleotide of claim 1 comprising a primer pair consisting of SEQ ID NO:16 and 17 and sequence that are at least 95% identical to SEQ ID NO:16 and 17 and hybridize to an MLV-related polynucleotide.
 8. The isolated oligonucleotide of claim 1 comprising a primer pair consisting of SEQ ID NO:19 and 20 and sequence that are at least 95% identical to SEQ ID NO:19 and 20 and hybridize to an MLV-related polynucleotide.
 9. (canceled)
 10. A method of determining viral content in a subject prior to or after undergoing a retroviral gene delivery therapy using an MLV-related virus, comprising: obtaining a sample from the subject; contacting the sample with one or more primer pairs as set forth in claim 1 under conditions suitable for nucleic acid amplification to obtain amplified products; contacting the sample with a one or more probes that hydridizes to the amplified product; detecting a hybridized product; indicating that the subject has viral content comprising an MLV-related virus.
 11. The method of claim 10, wherein the MLV-related virus is a recombinant retroviral vector used in gene delivery.
 12. The method of claim 10, wherein the MLV-related virus is an XMRV virus. 13-14. (canceled)
 15. The method of claim 10, wherein the MLV-related virus comprises a 5′ LTR, gag, pol, env genes, a regulatory domain 3′ of the env gene linked to a heterologous polynucleotide to be delivered and a 3′ LTR and a promoter for expression in mammalian cells in the 5′LTR.
 16. The method of claim 15, wherein the regulatory domain is an internal ribosome entry site (IRES).
 17. The method of claim 15 or 16, wherein the heterologous polynucleotide encodes a polypeptide having cytosine deaminase activity.
 18. The method of any one of claim 14, wherein the method monitors the spread of the MLV-related retroviral vector.
 19. The method of claim 18, wherein the method is carried out routinely over the course years.
 20. A method for detecting the presence of a viral agent in a sample comprising: measuring the amount of a polynucleotide in a sample using a quantitative polymerase chain reaction or other amplification process comprising oligonucleotide primer/probe combinations selected from the group consisting of: (i) SEQ ID NO: 1, 2 and 3; (ii) SEQ ID NO: 4, 5 and 6; (iii) SEQ ID NO: 7, 8 and 9; (iv) SEQ ID NO: 10, 11 and 12; and (v) primer pairs according to claim 9 and corresponding probes that have at least 95% identity to both XMRV and MLV.
 21. The method of claim 20, wherein the polynucleotide is DNA.
 22. The method of claim 20, wherein the polynucleotide is RNA.
 23. The method of claim 20, wherein the quantitative polymerase chain reaction is RT-qPCR.
 24. The method of claim 20, measuring detects a single copy of a viral agent related nucleic acid.
 25. The method of claim 20, wherein the viral agent comprises a MLV related virus and/or XMRV.
 26. The method of claim 20, wherein the sample is mammalian tissue or mammalian blood.
 27. (canceled)
 28. The method of claim 25, wherein the viral agent is a gene therapy vector.
 29. The method of claim 28, wherein the gene therapy vector is a replication-competent vector.
 30. The method of claim 20, wherein the method is performed prior to and/or subsequent to a therapeutic regimen comprising a gene therapy vector treatment.
 31. (canceled)
 32. The method of claim 20, wherein the method is performed to monitor the dosage of a therapeutic regimen comprising a gene therapy vector in a subject.
 33. The method of claim 28, wherein the gene therapy vector comprises a replication competent MLV vector. 34-37. (canceled)
 38. A kit for performing the method of any one of claim
 10. 39. A kit for performing the method of claim
 20. 40. A method of claim 10 for detecting <100 copies of MLV related DNA in a sample extracted from fixed histopathological sections.
 41. A method of claim 10 for detecting <100 copies of MLV related RNA in a sample extracted from fixed histopathological sections.
 42. A method of claim 10 or 20, wherein the method detects both MLV related virus and XMRV.
 43. A method of claim 10 or 20, wherein the method detects only MLV related virus and does not detect XMRV.
 44. A method of claim 10 or 20, wherein the method detects XMRV gag and MLV gag.
 45. A method of claim 10 or 20, wherein the method detects XMRV pol and MLV pol.
 46. A method of claim 10 or 20, wherein the method detects XMRV Env and MLV Env.
 47. A method of claim 10 or 20, for detecting either XMRV or MLV related virus in plasma or serum from a mammalian host.
 48. A method of selectively detecting MLV related viruses in humans and which does not detect XMRV comprising primers selected from the group consisting of: SEQ ID NO:10 and 11; SEQ ID NO:13 and 14; SEQ ID NO:16 and 17; SEQ ID NO:19 and 20; sequences at least 95% identical to the foregoing; and combination thereof, using a method of claim
 10. 49. A method of determining whether a human subject is at risk of having prostate cancer or chronic fatigue syndrome comprising utilizing primer pairs and probes as set forth in SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 or primer/probes as set forth in Table 1 or 2, to amplify polynucleotides in a sample from the subject, wherein the presence of an amplified product is indicative of a risk of prostate cancer or chronic fatigue syndrome.
 50. A method of screening a blood supply or tissue bank for infection by an MLV, MLV-variant or XMRV comprising performing an amplification reaction on the blood supply or tissue bank utilizing primers as set forth in SEQ ID NO:4, 5, 7, 8, 10, 11, 13, 14, or any of the primers in Table 1 or 2, and detecting an amplified product. 